Амплификатор Cfx 96, Cfx 384 Rev b (Bio-rad) Си

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Life Science Group

CFX96 and CFX384 Real


Time PCR Detection System

Service Manual

Part Number 10013582B BP-020495


PROPRIETARY NOTICE

Information contained in this manual is copyrighted by Bio-Rad Laboratories, Inc. None of the contents may be
reproduced in full or in part by any person without the prior written approval of Bio-Rad Laboratories, Inc. This
manual is intended to provide information to assist the qualified field or instrument service technician to repair,
maintain, and order replace parts for the instrument supplied. Every reasonable effort has been made to keep
the information in this manual current and accurate as of the date of publication or revision. However, no guar-
antee is given or implied that the manual is error-free or accurate about any specification.

© 2008 Bio-Rad Laboratories, Incorporated. All rights reserved.


Bio-Rad Laboratories Inc, Life Science Group
2000 Alfred Nobel Drive
Hercules, California 94547
Telephone: 1-800-424-6723

10013582A 04/08 i
About this manual This document is part of Life Science Group’s commitment to provide
you, the service professional, with adequate information to effectively
support Bio-Rad instruments. Additional copies of this service document
may be ordered using part number 10013582.

We welcome and appreciate any suggestions you may have to improve


our service documentation. Please address your comments or sugges-
tions to:

Technical Editor, Global Service Support Dept.


Bio-Rad Laboratories, Life Science Group
2000 Alfred Nobel Drive
Hercules, CA 94547
FAX Number: 510 741-5885

ii 10013582A 04/08
Revision Control List

Document: CFX96 and CFX384 Real Time System


Part Number: 10013582
Date Issued:

Each page of this manual has the catalog number, revision level and revision date. Subsequent revisions to the
manual will be indicated by changes to the revision level and revision date for the entire manual. A summary of
changes for all revisions is listed in the following table.

Page Business Changed


Revision Description Date
Number Process By
A All New Manual. Section 6 written by Chan Ahn BP-017344 Wahid 4/01/08
B All Revised Service Manual to include CFX384 Wahid 11/07/08

10013582A 04/08 iii


Table of Contents

Page

Section 1. Introduction
1.1 General Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.2 Service Philosophy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.3 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.4 Safety Certification and Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.5 Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2

Section 2. System Overview


2.1 About this Section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2 System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.3 Computer Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.4 OverView of the CFX96/CFX384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.5 CFX96/CFX384 Main PCBA Theory of Operation . . . . . . . . . . . . . . . . . . . . . 2-3
2.5.1 Basic Features and Functions: Refer to schematic Doc ID "D018880" . 2-3
2.5.1.1 DSP (U2): TI TMS320VC5509A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
2.5.1.2 CPLD (U1): Altera EPM1270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
2.5.1.3 (8051 )(15): Silicon Lab C8051F340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
2.5.1.4 Flash RAM (U4): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
2.5.1.5 SDRAM (U3): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.5.1.6 Stepper Motor Driver (U8-9): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.5.1.7 L6219DS (U10-11): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.5.1.8 LT3724 (U6): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
2.5.1.9 MC34063A (U2): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
2.6 CFX96/CFX384 Upper PCB theory of operation . . . . . . . . . . . . . . . . . . . . . . 2-8
2.6.1 Stepper motor connectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
2.6.2 Optical shuttle connector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
2.6.3 Voltage regulator for LED-ADC PCB . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
2.6.4 LED current driver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
2.6.5 Ambient temperature sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
2.6.6 Optical shuttle heater control signal . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
2.6.7 Connectors for optical shuttle, stepper motors, Main PCB . . . . . . . . . 2-10
2.6.8 Logic buffers for stepper motor limit switches, SPI bus . . . . . . . . . . . 2-10
2.6.9 Voltage regulator for LED-ADC PCB . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
2.6.10 LED current driver control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.6.11 Ambient temperature sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.6.12 U4 LED, heater control timer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.6.13 PCB layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11

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2.6.14 Thermal notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
2.7 CFX96/CFX384 Shuttle Transition PCB theory of operation . . . . . . . . . . . . 2-12
2.8 CFX96/CFX384 Detector PCB final theory of operation . . . . . . . . . . . . . . . 2-13
2.8.1 Topology selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
2.8.2 Noise and bandwidth considerations . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
2.8.3 Photodiode selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
2.8.4 Op amp U3 selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
2.8.5 Op amp U1 selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
2.8.6 Other component selection: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
2.8.7 Other noise sources: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
2.8.8 Power conditioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
2.9 CFX96/CFX384 LED-ADC PCB final of operation . . . . . . . . . . . . . . . . . . . . 2-17
2.9.1 Voltage reference and regulator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18
2.9.2 ADC selection and ADC input circuitry . . . . . . . . . . . . . . . . . . . . . . . . 2-18
2.9.3 SPI bus buffering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18
2.9.4 PCB layout considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18
2.9.5 PCB assembly considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18

Section 3. Installation
3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.2 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.3 Unpacking the CFX96 or CFX384 System . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
3.4 Installation Setup and Checklist of CFX96 or CFX384 System . . . . . . . . . . . 3-2
3.5 CFX96.CFX384 System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.5.1 CFX96/CFX384 System Power and cable Requirement . . . . . . . . . . . 3-3
3.5.2 CFX96/CFX384 PC and Software Requirement . . . . . . . . . . . . . . . . . . 3-3
3.6 Setting Up the CFX96/CFX384 System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
3.7 C1000 Base RAM Memory Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.8 CFX Manager Software Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.8.1 CFX Manager Software Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.9 System Power Up Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
3.10 System Checkout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-11
3.11 CFX96/CFX384 Catalog Parts and Accessories . . . . . . . . . . . . . . . . . . . . 3-11

Section 4. System Checkout


4.1 About this Section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.2 System Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1

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4.3 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.3.1 Tools and Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
4.4 Testing CFX96/CFX384 Alpha with Alpha Tester Board Fixture . . . . . . . . . . 4-3
4.5 C1000 Start up and Self test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
4.6 Firmware version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
4.7 C1000 Sensor Checker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
4.8 C1000 Diagnostic Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
4.9 CFX Manager Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12
4.10 Instrument System Test Software (IST) . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-16
4.11 IST Service Test Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-23

Section 5. Preventative Maintenance


5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.2 Tools and Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3 Preventative Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3.1 PM of CFX96 Reaction Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3.2 PM of C1000 Thermal Cycler Chassis . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
5.3.3 Maintaining Sufficient air flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
5.3.4 Perform System Checkout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

Section 6. Removal and Replacement


6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.2 Replacement / Adjustment Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.3 Removal and Replacement Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.3.1 Tools Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.4 Removing the CFX96/384 Housing Cover . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.5 Remove the Upper FCC Board and Cable Assembly . . . . . . . . . . . . . . . . . . 6-2
6.6 Removing the Main Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
6.6.1 Installing New Main Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
6.7 Removing the CFX Real Time Alpha . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
6.8 Base Plate Overlay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
6.9 Removing the XY stage assembly. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
6.10 Reference Spots Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-10
6.11 Front Motor Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-11
6.12 Front Motor Assembly Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-12
6.13 Lid Position Sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-13

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6.14 Lid Position Gear Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-14
6.15 Hinge Motor Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-14
6.16 Hinge Assembly Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-15
6.17 CFX96 Lid Heater Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-20
6.17.1 Plate Flag Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-22
6.18 CFX384 Lid Heater Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-23
CFX96/CFX384

Section 7. Adjustment and Calibration


7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.2 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.3 Test Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.4 Fx2 USB Test and Calibration Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.4.1 Service Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
7.4.2 Save Main board data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
7.4.3 Confirm and ReStore Main Board Data . . . . . . . . . . . . . . . . . . . . . . . . 7-7
7.4.4 ReConnect to USB Device . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-7
7.4.5 Read Alpha Block Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-8
7.4.6 Program Alpha Block to Real Time Block . . . . . . . . . . . . . . . . . . . . . . . 7-8
7.4.7 Display Sierra Instrument Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-9
7.4.8 Program Sierra Instrument type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-9
7.4.9 Do POST and Display Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-9
7.4.10 Move shuttle to a specified well . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-10
7.4.11 Turn ON specified Channel LED . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
7.4.12 Turn OFF all LEDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
7.4.13 Move to Shipping Screw Position . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
7.4.14 Set Shipping Screw Flag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
7.4.15 Clear Shipping Screw Flag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
7.4.16 Get shipping flag Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
7.4.17 Write Sierra Serial Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
7.4.18 Display Sierra(CFX) Serial Number . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
7.4.19 Display Shuttle Serial Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
7.4.20 Display All Faults Info . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
7.4.21 Clear All Faults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
7.4.22 Home X Axis Motor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
7.4.23 Home Y Axis Motor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
7.4.24 Display Stored X start Y start X lockdownoffset and Y lockdwonoffset 7-15
7.4.25 Set New X start Y start X lockdownoffset and Y lockdwonoffset . . . 7-16
7.4.26 Execute Stop and Read Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16

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7.4.27 Execute Flyover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17
7.4.28 XY Stage ReCalibration Sub Menu . . . . . . . . . . . . . . . . . . . . . . . . . . 7-18
7.4.28.1 Display current X Start, Y Start, X and Y lockdownoffset values . . . . 7-18
7.4.28.2 Move shuttle to the PIN CHECK position . . . . . . . . . . . . . . . . . . . . . . 7-19
7.4.28.3 Move Shuttle by one or ten microstep in +X direction . . . . . . . . . . . . . 7-20
7.4.28.4 Move Shuttle by one or ten microstep in -X direction . . . . . . . . . . . . . 7-20
7.4.28.5 Move Shuttle by one or ten microstep in +Y direction . . . . . . . . . . . . 7-21
7.4.28.6 Move Shuttle by one or ten microstep in -Y direction . . . . . . . . . . . . . 7-21
7.4.28.7 Display, confirm and write new X Start and Y Start values . . . . . . . . . 7-22
7.4.28.8 Move shuttle to the Shipping Screw position . . . . . . . . . . . . . . . . . . . . 7-22
7.4.28.9 Display, confirm and write new X and Y lockdownoffset . . . . . . . . . . 7-23
7.5 CFX96/CFX384 Firmware Upgrade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
7.6 C1000 and CFX96/CFX384 Firmware Upgrade Procedure . . . . . . . . . . . . . 7-24
7.6.1 Update C1000 PXA270 Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-25
7.6.2 Update C1000 HC12 Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-25
7.6.3 Update C1000 FX2 Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
7.6.4 Update CFX 96/CFX384 DSP Firmware . . . . . . . . . . . . . . . . . . . . . . . 7-26
7.6.5 Update CFX 96/CFX384 8051 SmartLid Firmware . . . . . . . . . . . . . . . 7-26
7.7 Installing the Drivers Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27
7.8 System Messages Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
7.9 Power Failure Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-29
7.10 Converting Conventional Alpha to Real-time Alpha Block . . . . . . . . . . . . . 7-30

Section 8. Troubleshooting
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.2 Troubleshooting the CFX96/CFX384 System . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.2.1 Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.2.2 Error Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-5
8.2.3 Troubleshooting Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-11

Section 9. Parts
9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.2 Parts Orders - US Domestic Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.3 Parts Orders - International Subsidiaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.4 Returning Defective Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.5 Recommended Spares . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

10013582A 04/08 vii


Table of Contents

Page
Section 10. Drawings
10.1 About this Section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
10.2 Drawings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
10.3 Schematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1

Section 11. Appendix


1
11.1 CFX96/ CFX384 Installation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-1
11.2 CFX96/CFX384 Operational Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-6

ix 10013582A 04/08
Introduction

Section 1
Introduction

1
1.1 General Information

2
This manual is the reference to be used for troubleshooting, repair, and maintenance of the CFX96/CFX384. It
is intended to be used by trained technicians and engineers familiar with safety precautions relative to working
with list of hazards. The procedures in this manual assume that the reader is familiar with the operation of the
Product Name. Complete operating instructions are contained in the Product Name instruction manual. Infor-

3
mation presented in the instruction manual is not repeated in this Service Manual unless there is a compelling
reason to do so.

1.2 Service Philosophy

4
This manual is designed to support all levels of a three level service philosophy. Field level service is the first
level of service, and uses the identification, removal and replacement of faulty field replaceable assemblies to
restore operations quickly and effectively. Regional service centers are the second level of service, where
faulty assemblies can be most effectively repaired at a central repair facility. The third level of service is
performed at our factory instrument service facility in Richmond, California, where additional service proce-

5
dures requiring resources not available at regional service centers are performed.

1.3 Safety

6
The CFX96/CFX384 contains the following Hazards:
• Hazardous voltages
• Thermally hot components

7
The following should be observed when servicing this unit:
• When power is required, the unit should be plugged into an outlet with a properly grounded receptacle. The
use of 2-prong plug adapters is not recommended and will void the safety certification of this product.
• The use of extension cords may compromise the safety of the operator and is not recommended.

8
• Ensure that fuses installed in the unit are of the correct rating.
• Ensure that none of the ventilation openings in the unit are blocked. Excessive heat buildup in the unit may
cause failures.

1.4 Safety Certification and Compliance 9 10 11


This Bio-Rad product is designed and certified to meet *EN61010-1 safety standards. Certified products are
safe to use when operated in accordance with the instruction manual. This instrument should not be modified
or altered in any way. Alteration of this instrument will void the warranty, void the EN61010-1 certification, and
create a potential safety hazard. This safety certification does not extend to other equipment or accessories
not EN61010-1 certified, even when connected to this product.
Bio-Rad is not responsible for any injury or damage caused by the use of this instrument for purposes other
than for which it is intended or by modifications of the instrument not performed by Bio-Rad or an authorized
agent.

10013582B 11/08 1-1


Introduction

Important: Instrument alterations expressly covered by the Safety Certification and


Compliance statement above include but are not limited to, using non-specified fusing,
addition or removal of electrical components, cutting traces or pins on PC boards, etc.

1.5 Conventions
The following conventions are used throughout this manual:
• Left and right sides of the unit are as viewed from the front, operator’s position, unless otherwise stated.
• Dimensions are in inches, unless otherwise stated.
• Pressure is in pounds per square inch.

1-2 10013582B 11/08


System Overview

System Overview

1
2.1 About this Section
This section of the manual provides an overview of the CFX96/CFX384 with specifications, computer

2
requirements, general description, followed by a theory of operation and circuit description.

2.2 System Specifications

3
To operate the CFX96 real-time PCR detection system, use the following power sources and cables:
• Input power. 100—240 VAC, 50—60 Hz
• Indoor use. Ambient temperature of 15oC—31oC. Relative humidity maximum of 80% (non-condensing)
• Operating temperature 5-40 °C

4
• Storage temperature 20-30 °C
• Humidity 0-95%, non condensing

5
2.3 Computer Requirements
This section describes the recommended PC computer requirements for the CFX96/CFX384.

6
System Minimum Recommended
Operating system Windows XP Professional SP2 and Windows XP Professional SP2 and
Above or Windows Vista Home Pre- Above or Windows Vista Home Pre-
mium and Above mium and Above

7
Drive CD-ROM Drive CD-RW Drive
Hard drive 10 GB 20 GB
Processor speed 1 GHz 2.0 GHz
RAM 1 GB RAM 2 GB Ram

8
Screen resolution 1024 x 768 with true-color mode 1280 x 1024 with true-color mode
USB USB 2.0, Hi-Speed port USB 2.0 Hi-Speed port
Operating system Windows XP, with Service Pack 2 Windows XP, with Service Pack 2
Internet browser
Software
Internet Explorer Internet Explorer
Microsoft Office Suite 9 10 11

10013582B 11/08 2-1


System Overview

2.4 OverView of the CFX96/CFX384

Figure 2-1: CFX96/CFX384 System

The CFX96/CFX384 system includes two components to run real-time PCR experiments:
• CFX96/CFX384 optical reaction module. This module includes the optical system to collect fluorescent
data and a block (inside) that heats and cools the PCR reactions quickly. Each optical reaction module
inserts into the thermal cycler base.

• C1000 thermal cycler base. The C1000 base supplies the power to CFX96/CFX384. CFX96/CFX384
uses the USB ports on back panel of C1000 to connect to a computer.

2-2 10013582B 11/08


System Overview

2.5 CFX96/CFX384 Main PCBA Theory of Operation

1
The CFX96/CFX384's Main PCB assembly performs the digital signal processing, memory management,
motion control, monitoring of all sensors and provide regulated power to the CFX96/CFX384 system.
Microprocessors from Analog Device and Freescale Semiconductor were considered before selecting TI's
TMS320VC5509A processor. The TMS320VC5509A was chosen primarily for its computational power (up to
400 MIPS @ 200MHz), sufficient internal RAM (128 Kb, or 64 Kwords), 6 DMA (Direct Memory Access) chan-

2
nels that enables hi-speed data acquisition requirement for CFX96/CFX384. Additional useful features of the
DSP are full speed USB, SDRAM interface, I2C, 3 SPI channels, calendar date and time timer, memory card
interface. This processor has two package versions -LQFP-144pins (Low Profile Quad Flat Pack) and BGA-
179 pins (Ball Grid Array) with 0.8 mm pitch. BGA package with such dense pitch raised some production
concerns, and so, LQFP package was chosen. The TMS320VC5509A is 16-bit fixed point DSP and has three

3
McBSP (Multi-channel Buffered Serial Ports) where each of them could be configured as SPI. In CFX96/
CFX384, McBSP #0 is configured as SPI to perform communications with ADC and EEPROM on the shuttle.

4
2.5.1 Basic Features and Functions: Refer to schematic Doc ID "D018880"
2.5.1.1 DSP (U2): TI TMS320VC5509A
a. Programming

5
i. Since the Boot program, Main program (Firmware) and X-Y calibration table (acceleration/
velocity profile) are stored in the external Flash ROM (U4), NO programming is required on
the DSP. However, optional programming through JTAG connector "J8" is available. See
section 4b.
ii. Once "boot loader" is programmed in the Flash ROM, future field installation and/or upgrade

6
of main program is possible without removing board from CFX96/CFX384 instrument via
Everett USB.
b. DMA Channels
i. CH 0 is used to transfer of 16 bit A/D conversion result to memory buffer.

7
ii. CH 1 is used to transfer of A/D convert commands from fixed memory location to 16 bit A/D
chip.
iii. CH 2 is unused

8
iv. CH3 is used to transfer of timing period values to CPLD step-A/D timer from memory buffer
(profiled stepper moves)
v. CH 4 is unused
vi. CH 5 is used to transfer of command responses to transmit UART in CPLD
c. Clock speed
i. TMS320VC5509A is capable of running 108, 144 and 200MHz where the DSP core voltage
9 10 11
determines the operating clock speed. CFX96/CFX384 is configured to operate at 144MHz.
Hence, DSP core voltage is set at 1.35V (U13).
d. I2C Communication
i. Used to transmit and receive data to/from the IO expander which controls selection of LED's
and LM75 temperature sensor located in the UPPER board. A "100 kbit/sec" serial bus with
clock (I2C-SCL) and data (I2C-SDA) signals with 7bit addressing. The address and the data
bytes are sent most significant bit first where the "start" bit being first followed by the 7 bit
address of the slave it wishes to communicate.

10013582B 11/08 2-3


System Overview

e. SPI Communication
i. Used to send and receive data to/from the 16bit/6 channel ADC and EEPROM located in the
ADC/LED board. The DSP serves as the Master and controls all communication. The master
(DSP) drives the clock (DSP_SCLK) line for the serial data IN and OUT. Data is sent out on
the DSP_SDO line, most significant bit first and data is read on the DSP_SDI line, also with
most significant bit first. The Master also determines when data is sent and received through
DSP_BUSY line. Data transfer can be as fast as 5 million bit/sec. Device selections
"CS_EE_CPLD and CS_ADC1 are controlled by the CPLD.

2.5.1.2 CPLD (U1): Altera EPM1270


a. Programming
i. CPLD program may be programmed on board using Altera emulator thru JTAG (J9) connector
or pre-programmed the IC thru programming device prior to installation to the board.
b. Page Register Address
i. Since the DSP version selected is LQFP-144 package, only pins for lower 14 address lines
out of 20 are available. To fully optimized memory capacity, an external page register is
needed for FLASH addressing. This page register is implemented in CPLD (Complex Pro-
grammable Logic Device).
c. Timing Generation
i. Generates microstep pulse, and pulse interrupt line for DMA and/or ISR triggering.
ii. Outputs microstep pulse to enables stepper(s).
iii. Generates reload interrupt to allow DMA of ISR load of continuously varying profiled move
delays.
d. UART Serial communication
i. "MAIN_TX" and "MAIN_RX" signals are the main communication link between CFX96/
CFX384 and Everett.
ii. UART is shared with the "Smartlid" (8051) and DSP thru the CPLD. The DSP has total control
of the UART during normal operation. For the Smartlid control of the UART, the Smartlid
asserts "CS0_8051CONTRL" signal LOW to send request for control. The DSP in return,
acknowledges the request by asserting "CS1_8051_ACK" signal LOW. At this point, the
Smartlid has now control of the UART. However, if the Smartlid doesn't assert an acknowl-
edge signal back within 10 mSec, the DSP takes back control of UART. The UART run's at
baud rate of 57.6 Kbps.
e. X-Y motion control
i. ST_*_DIR, ST_EN_*DRV, ST_STEP_* and ST_*-RST signals are control signals to Stepper
Motor drivers (U8-9) for the X&Y scan axis. See "Stepper Motor Driver" section for each sig-
nals functional information.
f. Optical sensor
i. *LIM+ and *LIM- signals are inputs from limit sensors of the X-Y axis.
g. Chip select enable
i. CS_ADC1, CS_EE_CPLD, LED-PWR_EN-L and HTR-PWR-EN_L signals are used to select
the device to enable.

2-4 10013582B 11/08


System Overview

2.5.1.3 (8051 )(15): Silicon Lab C8051F340


a. Programming

1
i. SmartLid program and Boot program may be programmed on board using Silicon Lab emula-
tor thru JTAG (J5) connector or pre- programmed the IC thru programming device prior to
installation to the board.
ii. "SmartLid" firmware upgrade can be performed thru JTAG or UART once "Boot loader" is

2
installed.
b. Memory Location
i. ISR vectors are stored from location 0x0000 to 0x0100.
ii. Boot Program is stored in memory location 0x100 to 0x3FFC. Boot program version number

3
is stored in memory locations 0x3FFC-0x4000.
iii. SmartLid Program is stored in memory location 0x4000 to 0xBFFE. CRC is stored in memory
location 0xBFFE-0xC000. SmartLid program present key is stored in memory location
0xC000-0xC200.

4
iv. Memory locations from 0xC200 to 0xFC00 are reserved for calibration data storage.
c. Smart Lid control
i. HTR_*, FRNT_*, HINGE_* signals are used to control operation of the DC motor drivers.

5
d. Smart Lid sensors
i. ENC_* signals are encoder signals used to monitor the position/location of the HTRPOS and
HINGE. It is also used to monitor the HINGE's opening/closing time to determine if there is an
object obstructing the HINGE motion.

6
ii. LIMIT_* signals are input from end-limit sensors of the DC motors.
e. Serial communication (UART)
i. MAIN_TX and MAIN_RX signals are shared between DSP (through CPLD) and 8051 as com-

7
munication link Everett via RS3232 (U17).
ii. During Smart Lid operation, DSP gives up the UART port to 8051 using "CS0_8051CONTRL"
as handshaking signal and "CS1_8051_ACK" acknowledge signal. See CPLD section.
f. I²C communication.

8
i. 8051-I2C_DATA and 8051-I2C_CLK signals are used to communicate with Everett to monitor
lid status during normal operation. It is also the primary means of communications for "Non-
Real Time Moto Lid" configuration.

2.5.1.4 Flash RAM (U4):


a. 4Mbit (256k x 16) Flash ROM primarily used as storage of Main program, boot program, calibration
table, and motion (acceleration and velocity) profile of "step & repeat" and "fly over" modes of scan
9 10 11
operation.
b. CFX96/CFX384's Main program and Boot program may be programmed on board thru JTAG (J8)
connector using Code Composer Software from TI and an emulator from Digital Spectrum. The pre-
ferred option is to pre- program the IC thru programming device prior to installation to the board.
c. Memory location
i. Boot Program is stored in memory location 0x23C000- 0x23C7FF. Boot program version
number is stored in memory locations 0x23C7FF-0x23CFFF.

10013582B 11/08 2-5


System Overview

ii. Main Program is stored in memory location 0x200002-0x208000. Main program present key
is stored in memory location 0x200000-0x200001.
iii. Memory locations from 0x228000-0237FFF are reserved for calibration data storage.

2.5.1.5 SDRAM (U3):


a. 64Mbit (4M x 16) SDRAM is used as buffer to store raw data of scan read before being retrieve. Dur-
ing normal operation, acceleration and velocity profile is also loaded here from the Flash ROM until
power is shut down.

2.5.1.6 Stepper Motor Driver (U8-9):


a. The A3984 is a complete micro-stepping motor driver with built-in translator for easy operation. It is
configured to operate bipolar stepper motors in sixteenth-step modes, with an output drive capacity of
up to 35 V and ±2 A.
b. Reset
i. Reset input sets the translator to a predefined Home state and turns off all of the DMOS out-
puts. All STEP inputs are ignored until the RESET input is set to high.
c. Step input
i. A low-to-high transition on the STEP input sequences the translator and advances the motor
one increment. The translator controls the input to the DACs and the direction of current flow
in each winding.
d. Direction
i. This determines the direction of rotation of the motor. When low, the direction will be clockwise
and when high, counterclockwise. Changes to this input do not take effect until the next STEP
rising edge
e. Current Limit
i. The maximum value of current limiting is set by the selection of Rs (ie: R115//R20) and
2.7VREF. The transconductance function is approximated by the maximum value of current
limiting, Itrip max which is set by: Itrip = VREF / ( 8 × RS ).
f. MicroStep resolution
i. The micro step resolution is set by the combined effect of inputs MS1 and MS2 input pins of
A3984. CFX96/CFX384 is configured to operate in 1/16th step resolution (MS1 - MS2 = HI)

2.5.1.7 L6219DS (U10-11):


a. The L6219DS motor driver is designed to drive both windings of a bipolar stepper motor or bi-direc-
tionally control two dc motors. Both bridges are capable of sustaining 45 V and include internal pulse-
width modulation (PWM) control of the output current to 750 mA.
b. Logic Control
i. Two logic level inputs (l0 and I1) allow digital selection of the motor winding current at 100%,
67%, 33%, or 0% of the maximum current.
c. Direction
i. The PHASE input to each bridge determines the direction of motor winding current flow.
d. Current Limit
i. Output current is sensed and controlled independently in each bridge by an external sense
resistor RS (ie: R23), internal comparator, and monostable multivibrator. When the bridge is

2-6 10013582B 11/08


System Overview

turned on, current increases in the motor winding and it is sensed by the external sense resis-
tor until the sense voltage (VCOMPIN) reaches the level set at the comparator's input:

1
Itrip = VREF(3.3V)/10*Rs

2.5.1.8 LT3724 (U6):


a. DC-DC 24V regulator with current limited to 3A max.

2
i. Primarily used to power the Stepper motors and DC motors.
ii. Also provides power to the Upper board.

2.5.1.9 MC34063A (U2):

3
a. DC-DC 5V regulator with current limited to .5A max.
i. Primarily used to provide power to Optical sensors.
ii. Input to 3.3V regulators

4
iii. Power to Upper board.

5
6
7
8
9 10 11

10013582B 11/08 2-7


System Overview

Figure 2-2: Main Board Block Diagram

2.6 CFX96/CFX384 Upper PCB theory of operation


Theory of operation:

Refer to schematic D019704, Schem, Upper PCB, CFX96/CFX384

Overview:
Upper PCB carries:
a. Connectors for optical shuttle, stepper motors, Main PCB

2-8 10013582B 11/08


System Overview

b. Logic buffers for stepper motor limit switches, SPI bus

c. Voltage regulator for LED-ADC PCB

1
d. LED current driver control

e. Ambient temperature sensor

2
f. Optical shuttle heater control

3
2.6.1 Stepper motor connectors
Stepper motor connectors are J41, J42, J43 for Y-axis, J9 for X axis. RC snubber networks on each motor
power line to motor ground (R52, R42, R43, R47, C35, C25, C26, C23 for X axis, R50, R48, R51, R47, C33,
C31, C34, C30 for Y axis) conduct on motor switching transients for reduced EMI. Motor power lines and

4
motor power ground connect to Main PCB connector pins P12-29,30,31,32 for X axis, P12-35,36,37,38 for Y
axis, P12-27,28,33,34,39,40 for motor power ground. Limit switch inputs are filtered by C14,15,17,18 and
buffered by U8 logic inverters for noise immunity.

5
2.6.2 Optical shuttle connector
Optical shuttle connector is J8, carrying SPI bus pins J8-4/SCLK_CBL, J8-6/SDI_CBL, J8-9/SDO_CBL, SPI
device control lines J8-8/CS_ADC_CBL, J8-11/BUSY_CBL, J8-12/CS_EE_CBL, as well as LED-ADC
voltage regulator, LED and shuttle heater circuits described below. Signal names _CBL are buffered by logic

6
inverters in U2, logic inverters in the optical shuttle restore correct signal polarity; signals are buffered for
noise immunity. Buffer inputs are sourced from Main PCB connector pins P12-1,3,5,7,9,12.

7
2.6.3 Voltage regulator for LED-ADC PCB
Voltage regulator for LED-ADC PCB is switching voltage regulator IC U9 and associated components. Input
voltage from P12-25 is +24 (Main PCB regulator tolerance is 23 - 25V). R49 and R46 and U9 voltage refer-
ence set output voltage at +VA and -VA to 1.25V*(1+R49/R46) or 8.1V nominal. U9 senses voltage at R46/

8
R49, switch output is filtered by D2, L1-1,2, C24 for +VA, by C32, D1, L1-3,4, C16 for -VA. R35, R36, C20
provides additional filtering for +VA, R34, R33, C19 for -VA. +VA, -VA connect to J8-22,21.

2.6.4 LED current driver


LED current driver sources current to optical shuttle cable J8-20, with six LED anodes connected in
common, and sinks current from one of six LED cathodes at J8-14,15,16,17,18,19 by Q3,4,5,6,7,8,
9 10 11
controlled by I2C bus port expander U7 through Main PCB pins P12-11 I2C-SDA (data), P12-13 I2C-SCL
(clock). LED current level is controlled by I2C 8-bit DAC U5, opamp U3, pass transistor Q1 and associated
components; current is sensed by R22 and compared to scaled DAC output. LED current on/off timing is
controlled by P12-18 ENLED, which drives U8-F, U4-B, Q2 and associated components to short scaled DAC
output to ground or not; current switches off with ENLED low or after ENLED is high for 17 - 34ms. LED
current power source is +5.5V from linear regulator U10 and associated components with +24V input. DAC
power source and voltage reference is U6 and associated components with +3.3V output and +5.5V input.

10013582B 11/08 2-9


System Overview

2.6.5 Ambient temperature sensor


Ambient temperature sensor is U1, controlled by I2C bus. U1-3 connects to P12-15 to drive fan switch on
Main PCB.

2.6.6 Optical shuttle heater control signal


Optical shuttle heater control signal from Main PCB at P12-17 (ENHTRPWR) drives U4-A, Q9, Q10 and
associated components; rising edge logic signal at U4A-1 turns Q9 off and Q10 on for 17 - 34 ms, contin-
uous heating power requires repeated rising edges at 17ms or faster. Heater resistor power is sourced at
+40V pin P12-26 to optical shuttle J8-1, returns on J8-2 and sinks on Q10C to motor power ground.

2.6.7 Connectors for optical shuttle, stepper motors, Main PCB

P12 was chosen for secure engagement with Main PCB mating connector, however no second source is
known. 1mm pitch flat flex cable was chosen for mechanical durability and ampacity, leading to J8, J9
connector choices. J42, J43 were chosen for compatibility with chosen cabling. J41 was chosen for multiple
sourcing, mechanical durability and ampacity.

2.6.8 Logic buffers for stepper motor limit switches, SPI bus

Buffers are Schmitt type which improve noise immunity due to input logic threshold hysteresis. Resistors
R2, R4 - R8 decouple buffer pins from electromagnetic interference.

2.6.9 Voltage regulator for LED-ADC PCB

Multiple sourcing was a major factor in component selection for this regulator, and all components are
multiple sourced. U9 has a low maximum switching frequency and requires more and larger external
components than modern choices but is one of only two widely sourced DC-DC converter ICs with inte-
grated power transistor, and is used in Main PCB for higher-power application with external power switch.

R33 - R36 limit current in fault condition and will tolerate continuous short circuit as well as provide additional
noise filtering. Voltage drop on these resistors from LED-ADC and Shuttle Transition PCB supply current
were considered.

Coupled inductor L1 allows negative output from positive input supply with lower switching noise and less
component stress than charge pump inverters. This circuit requires positive output current greater than
negative output current for correct regulation which is provided by scaling of R49 and R46.

C32 limits voltage switching spikes on D1 cathode from L1 leakage inductance that can exceed diode
reverse voltage rating.

2-10 10013582B 11/08


System Overview

2.6.10 LED current driver control

1
LED current rise time is largely dependent on U3 rise time and programmed current level, 100us or less is
expected at normal (40mA) current levels.

LED selection is controlled by Main PCB DSP firmware through U7, a multiple-sourced I2C port expander
with 100kHz maximum bus clock. ENLED controlled by Main PCB CPLD is required, 100kHz speed is OK

2
for LED selection but too slow for accurate on/off timing.

Linear regulator U10 is low cost and multiple sourced but inefficient; with 23% total LED duty cycle and 25C
ambient, LED current must be less than 330mA. This is OK for CFX96/CFX384 but a more efficient design

3
may be needed if CFX384 requires more than 330mA.

2.6.11 Ambient temperature sensor

4
Chosen location is close to plastic enclosure and away from warm components on this PCB.

5
2.6.12 U4 LED, heater control timer

U4 limits on time of LED and shuttle heater in case of firmware or digital circuit malfunction. Timing range is
(0.39 to 0.56)*R*C, nominally 24ms, or 17 - 31 ms with component tolerances. U4 contains a comparator

6
with hysteresis, logic gates and analog switches that allow timing C to charge through R and logic output to
switch when logic input is switched until comparator is triggered, after which C is discharged and logic output
switches.

7
For LED, rising edge of ENLED triggers U4-B, causing Q2 to turn off and DAC voltage to pass to U3-A.
ENLED transition to logic low within 17ms after rising edge resets U4-B and turns Q2 on; U4-B times out if
ENLED stays high for longer than 17ms.

For heater, falling edge of ENHTRPWR triggers U4-A, causing Q9 to turn off and Q10 to pass heater current

8
until U4 times out in 17 - 31ms.

2.6.13 PCB layout

PCB is double sided with components and almost all signal traces on side facing stepper motors, and two
9 10 11
ground plane areas on outer side, one plane for signal power and another for stepper motor power; noise
performance is similar to 4-layer PCB with lower cost but layout work is more difficult and available compo-
nent area is reduced. Signal traces and stepper motor traces are aligned with respective ground planes.
SPI bus traces are grouped together with interleaved ground traces and separated from motor traces where
possible. LED driver DAC circuits are placed between SPI and motor trace areas. LED driver switch
circuits are close to J8. LED-ADC PCB and LED driver voltage regulators are in corner near J8 and LED
driver switch circuits.

10013582B 11/08 2-11


System Overview

2.6.14 Thermal notes

U10 is the only warm IC in normal use. U9 can be warm with LED-ADC short circuit.
R37,42,43,47,48,50,51,52 are warm when motors are energized.

2.7 CFX96/CFX384 Shuttle Transition PCB theory of operation

Refer to schematic D025966, Schem, Shuttle Transition, CFX96/CFX384.

Figure 2-3: Shuttle Assembly

Overview:
Shuttle Transition PCB carries:
a. Connector for optical shuttle
b. Flat flex cable for connection to Upper PCB
c. Logic buffers for SPI bus
d. Voltage regulator for logic buffers

Theory of operation:
1. P10 carries 2mm header that plugs into LED-ADC PCB J10. Pins carry all required signal and power cir-
cuits, refer to LED-ADC PCB theory of operation for description.

2. 1mm flat flex cable solders to J1. Cable strain relief is assembled to PCB. Refer to Upper PCB theory of
operation for description of connected circuits.

3. U1 and R1-6 buffer SPI bus logic circuits to complement Upper PCB U2 buffers, refer to Upper PCB theory
of operation for description.

4. Linear regulator U2 supplies 3.3V to U1. C1 and C2 provide input and output decoupling.

2-12 10013582B 11/08


System Overview

5. PCB layout is double sided with ground plane on outer side beneath U1 input and output circuits. Area

1
above P10 carries ground plane to block light for reliable optical limit switch operation.

2
3
4
5
Figure 2-4: CFX96/CFX384 Shuttle

2.8 CFX96/CFX384 Detector PCB final theory of operation

6
Overview:
Detector PCB accepts light energy with three photodiodes as input, and supplies output voltages for three A/D
(analog-to-digital converter) inputs.

7
Theory of operation - summary:

Refer to schematic D019284, Schem, PCB, Detector, CFX96/CFX384. One channel is described, the other

8
two are identical.

a. Photodiode D3 converts light energy to current. The current is converted to voltage by opamp U3 and
resistors R11, R15. Ratio of U3 output voltage to input current is Rf = R11+R15 or 20*10^6 or 20Meg. C4
limits amplifier bandwidth and prevents amplifier oscillation with D3 junction capacitance (note: C4 function
is not tested). 9 10 11
b. U3 output voltage is negative, and is converted to a positive voltage by U1 and resistors R3, R5; U3 gain is
R3/R5 or 8.25. Output voltage range is approximately 100mV to 3.2V. U1 output connects to R4, part of
RC filter for A/D input (C is on LED-ADC PCB), J1-3 connects output voltage to LED-ADC PCB. The other
two outputs are at J1-5 for D4, J1-4 for D5.

c. Ratio of U3 output voltage to photodiode current is 20Meg*8.25 or 165 Meg.

d. R2 and R6 maintains output voltage greater than zero with no light. U1 inverting input is at +VA*(R6/
(R6+R2)) or 10.6mV, output offset voltage is (8.25+1)*10.6mV = 98mV, or 1960 counts after A/D conver-

10013582B 11/08 2-13


System Overview

sion (1346 - 2617 counts worst case). This voltage represented in A/D counts is called "dark counts" or
"dark value".

e. D1 clamps U1 input to prevent abnormal output at high light levels (where output voltage would exceed
3.29V if possible).

f. U3 is powered from +VA (nom. 3.29V), -VA (nom. -1.64V). U1 is powered from +VA, AGND. Power is
sourced from LED-ADC PCB, +VA at J1-1, J1-8, -VA at J1-7. C3, C2 bypass +VA, -VA.

2.8.1 Topology selection

Topology in summary consists of two stage amplifier - transimpedance amplifier (TIA) (op amp U3, Rf, C4)
converting photocurrent from D3 to voltage at U3 output, followed by inverting voltage amplifier (op amp
U1A, R5, R3). Photodiode cathode is connected to ground so TIA output is negative, requiring inverting
amplifier for positive output. Offset is applied by R2, R6 to ensure output with no light within A/D converter
span.

2.8.2 Noise and bandwidth considerations

1. Bandwidth - lower bandwidth gives lower noise and longer rise time to a step input. Bandwidth is
defined by RC time constants of C4*(Rf) and R4*(2.2uF on LED-ADC PCB). Rise time is approximately
2.2*SQRT((C4*(Rf))**2+(R4*2.2uF)**2) or 654usec.
Measured rise time matches to about 10%.
Noise testing over 1ms integration time of a detector with 350usec gave 20% higher noise than a
detector with 650us risetime.

2. Resistor noise - proportional to square root of resistor value (R11+R15). Signal is proportional to resis-
tor value so signal/noise ratio is proportional to square root of resistor value. Increasing resistor value
too much will limit bandwidth and input for full scale response, so these factors will limit S/N. Resistor
noise dominates in an optimal design. Resistor values above 10Meg are specialty items especially in
surface mount packages.

3. Input voltage noise of op amp U3 (en) - photodiode shunt capacitance (Csh), from junction capacitance
of D3, and C4 define input voltage noise gain of 2 at f = 1/(6.28*(Rf)*(Csh+C4)). With the schematic val-
ues and Csh=1700pF, f=4.6Hz. This noise gain increases linearly with frequency until limited by op amp
open-loop gain and downstream low-pass filtering Noise gain can be made smaller with smaller Csh
and/or larger C4; smaller Csh requires photodiode with smaller active area or higher cost, larger C4
reduces bandwidth. (en) is a factor in op amp selection if noise gain cannot be reduced so that (en)
referred to output is negligible compared to resistor noise. (en) in the selected op amps is low but not
negligible in this design. Datasheet (en) is guaranteed at 1kHz only, datasheet typical (en) at lower fre-
quencies suggests likely worst-case at lower frequencies but measurements in the application are
required for predicting worst-case performance.

2-14 10013582B 11/08


System Overview

4. Thermal drift - photodiode shunt resistance decreases 12% per °C increase, causing baseline drift since
U3 input offset voltage vos is amplified by 1+(Rf)/Rsh. U3 input bias current ib doubles per 10°C, and ib
is converted to voltage along with photocurrent, so low input bias current at 25C is required to control

1
baseline drift at 45°C.

2
2.8.3 Photodiode selection

1. Active area - smallest area compatible with optical and mechanical design, larger area increases shunt

3
resistance and capacitance.

2. Packaging -metal can with glass window is compatible with mechanical design, plastic packages are too
close to PCB surface and too far from focal point.

4
3. Electrical - tradeoff exists between cost, shunt resistance (resistance in parallel with ideal diode) and
shunt capacitance. High shunt resistance or low shunt capacitance is available for about the same cost,
both are available at higher cost. Required bandwidth allows higher shunt capacitance so lower shunt

5
resistance is available at lower cost. Higher shunt capacitance increases amplifier input voltage noise
transferred to output, lower shunt resistance increases amplifier input offset voltage drift transferred to
output. Selection for higher shunt resistance than worst-case spec is required in this design at slightly
higher cost.

6
4. Manufacturers - Hamamatsu is the current approved vendor. UDT is another vendor with a similar
device.

7
2.8.4 Op amp U3 selection

1. Electrical - en, ib and vos are important as discussed above. Op amps with en < 10nV/?Hz, ib < 1pA at

8
25°C and < 75pA at 85°C, vos < 0.2mV at 25°C and dvos/dT < 5uV/°C are suitable. ib and vos are
worst-case, en is typical at 1kHz so component evaluation is required to confirm en performance.

2. Packaging - Suitable surface mount packages are SO8 and SOT23-5. SOT23-5 is small enough to
allow components on one side, SO8 needs components on both sides with the available area.
9 10 11
3. Manufacturers - TI/Burr-Brown OPA124 in SO8 was the original selection meeting the electrical specs
but became difficult to purchase. Analog Devices AD8605, Linear Technology LTC6240 and National
Semiconductor LMP7705 were found to have equal or better performance for ib and vos vs, LTC6240
has equal performance for en but AD8605 and LMP7705 are somewhat lower performance

10013582B 11/08 2-15


System Overview

2.8.5 Op amp U1 selection

U1 characteristics are less critical than U3, vos < 3mV, dvos/dT < 6uV/°C, ib < 100nA are adequate.
Minimum output must not exceed 50mV. U3 output is negative, if it is less than -0.4V, then U1 output will be
at +VA and U1 inverting input will be less than AGND. Output of many op amps under this condition will then
switch to AGND, this is called overload phase reversal. The types selected do not normally exhibit overload
phase reversal, but not all of them are specified as such, so D1 is included to guarantee no phase reversal.

2.8.6 Other component selection:

R11, R15 are standard commercial 0805 resistors, with 100ppm/°C temperature coefficient.

C4 is 0805 C0G ceramic capacitor with lowest piezoelectric activity of commercial ceramic capacitor types.

2.8.7 Other noise sources:

1. Electrostatic/capacitive noise - D3 pin 1 is highly sensitive to charge transfer by electrostatic or capaci-


tive coupling. The outer side and most of the inner side of the PCB is copper connected to AGND, but
pin 1 is exposed on the outer side. A metal shield plate covers the photodiode pins to control this noise
source.

2. PCB bulk and/or surface leakage noise - PCB layout surrounds pads/traces connected to D3 pin 1 with
copper and removes soldermask as much as possible to control surface leakage, but surface contami-
nation will increase noise as noted earlier.

3. Microphonic noise - the assembly is known to be somewhat sensitive to mechanical shock/vibration, this
has not been shown so far to add excess noise in final assembly testing.

4. "Cosmic ray" noise - noise pulses at intervals of a few seconds to a few minutes appear with photo-
diodes installed and covered to block light, and do not appear with photodiodes removed. This is most
likely due to particles or photons from radioactive decay or cosmic rays reaching the photodiode, similar
photodiodes and circuits are used for gamma ray detection.

2.8.8 Power conditioning

+VA, -VA is bypassed by C3, C2 and regulated on LED-ADC PCB. Both Detector PCBs in a shuttle are
connected in parallel to +VA, -VA.

2-16 10013582B 11/08


System Overview

2.9 CFX96/CFX384 LED-ADC PCB final of operation

1
Overview:
LED-ADC PCB carries:

a. LEDs for illuminating DNA test samples to stimulate fluorescence.

2
b. A/D (analog-to-digital converter) for converting voltages from Detector PCB to digital data.

c. EEPROM, non-volatile memory for storage of calibration constants.

3
d. Voltage reference for A/D IC.

e. Voltage regulators for A/D, EEPROM and Detector PCBs power.

4
f. Heater resistors and thermistor for optical housing temperature regulation.

Theory of operation:
Refer to schematic D019565, Schem, LED-ADC PCB, CFX96/CFX384.

5
1. LEDs (LED0 thru 5) are mounted with controlled height. LEDs are of five different colors, and each loca-
tion must have the correct color. LED current is sourced from Upper PCB, through pins J10-3,4,5,6,7,8,10.

6
2. U3 is A/D IC. A/D Channels are inputs with approximate range of 0 - 3.29V, conversion scale factor of
19938 counts/V nominal, 18839 - 40124 counts/V worst case and is powered with 3.39V at pins U3-12,20,
and voltage referenced at pin U3-11. A/D Channel 0,1,2 are connected to J14-4,5,6. A/D Channel 3,4,5
are connected to J15-4,5,6. A/D Channel 6,7 are connected to thermistor TH1-1. C5,6,8,9,10,11 are part
of RC filters for limiting A/D input bandwidth, R is on Detector PCBs. C12 is part of RC filter with R3 and

7
thermistor. Output is sent over SPI bus pins J10-9/SCLK, J10-15/SDO, J10-13/BUSY. Conversion com-
mands are received over SPI bus pins J10-9/SCLK, J10-11/SDI, J10-17/CS_ADC.

3. U2 EEPROM stores 256k bits of data. Input is received over SPI bus pins J10-9/SCLK, J10-11/SDI, J10-

8
19/CS_EE. Output is sent over SPI bus pins J10-9/SCLK, J10-15/SDO.

4. D1 is adjustable voltage reference IC, with output at D1-1 buffered by Q1. Output voltage at +VREF is set
by R7, R13, R11. R7, R12 and C2 are RC filter for A/D voltage reference input.

5. +VREF is reference voltage for Detector PCB voltage regulators. Detector PCB positive supply voltage +V
9 10 11
is regulated by U1-A and Q4 and connected to pins J14-1,8 and J15-1,8, output voltage is practically the
same as +VREF. Detector PCB negative supply voltage -V is regulated by U1-B and Q3, output voltage is
VREF*(R6/R5); R9 aids Q3 current sinking with transient loads. A/D IC supply voltage is sourced through
Q2; voltage is slightly higher than +VREF due to R7.

6. Optical housing is heated by R1, R2, R14, R15 connected to J10-21,22; power is controlled at Upper PCB.
Optical housing temperature is sensed by 10kohm thermistor connected to TH-1,2. Thermistor is powered
by +V through R3.

10013582B 11/08 2-17


System Overview

Theory of operation - further information:

2.9.1 Voltage reference and regulator

Using +VREF as voltage reference for both ADC and voltage regulators, and opamp-based voltage regula-
tors provides tracking or close matching between ADC voltage reference and ADC, op amp supply voltages
while using multiple sourced parts. The ADC input span is 0 - VREF and VREF <= VCC, so the tracking
maximizes available span. ADC VCC is 0.1-0.2V greater than VREF due to R7 voltage drop and Q4 Vbe
and Ie <= Q1 Vbe and Ie, ensuring ADC analog input voltages less than VDD. Fewer components would be
needed if close-tolerance ADC reference and voltage regulators were used, but these are single-sourced.

2.9.2 ADC selection and ADC input circuitry

ADC , TI ADS8344, and ADC analog input circuitry is the same as used in Chromo4 and was selected for
this reason. Programmed sample rate is 50000 samples/sec, requiring SPI SCLK = 24*50000 = 1.2MHz.

2.9.3 SPI bus buffering

SPI bus lines are buffered by Shuttle Transition PCBA which connects to J10. Chromo4 used unbuffered
SPI bus with ESD protection diodes, this PCBA does not have these diodes due to buffering.

2.9.4 PCB layout considerations

PCB layout is on 4 layers.

Solid ground plane is on one inner layer and significant ground plane area is on other inner layer and outer
layer facing away from shuttle block without components. Outer layer facing towards shuttle block carries
components and has no ground plane. Ground pin locations of ADC and ADC input filter and power bypass
capacitors was examined to ensure solid ground plane under these parts.

Component layer carries most ADC input traces and heater power traces, with solid ground plane inner layer
immediately below it. The other inner layer carries LED and ADC, op amp power traces, avoiding coupling
of LED power traces to ADC input traces. The other outer layer carries SPI bus traces as much as possible
to avoid coupling to ADC input traces.

2.9.5 PCB assembly considerations

Assembly dimensions of LEDs and heater power resistors are closely specified in the assembly drawing to
avoid component soldering during assembly to shuttle block.

2-18 10013582B 11/08


Installation

Section 3

1
Installation

3.1 Overview

2
This section of the manual guides you through the installation and setup of the CFX96 and CFX384 Optical
Module System. An Installation report should be completed with each installation checkout. A checklist shall
provide verification that the instrument passed the requirements in the Installation section. Checklists for

3
CFX96 is provided in the Appendix section. This section represents the Installation of the instrument.

3.2 Safety

4
Electrical
High Voltage Circuits: The C1000 cycler contain high voltage circuits. Instrument must have power discon-
nected before servicing.

5
6
7
Thermal
Thermally Hot Components: The sample block and lid heater of the C1000 and S1000 can reach temper-
atures of 100°C during operation of the instrument. The heated lid should remain closed at all times during
operation to prevent accidental skin burns. Always allow the sample block to return to its idle temperature

8
before opening the lid and removing samples. Take caution to avoid touching the heated lid when lid temper-
ature control is on. When placing or removing samples, open the heated lid all the way up to allow maxi-
mum clearance and to avoid the heated lid from falling on hands. Make sure that no object obstructs the lid
before opening it. Instrument must be allowed to cool to safe temperature before servicing.

9 10 11

10013582B 11/08 3-1


Installation

Electro Static Discharge (ESD)


The C1000 and S1000 contain ESD sensitive parts. Observe ESD precautions when handling these parts.
Wear grounding wristband and store parts in ESD shielded bags.

3.3 Unpacking the CFX96 or CFX384 System


This section describes unpacking the CFX96/CFX384 system.
1. Remove all packing material and connect components on a flat, dry surface near an appropriate electrical outlet.
2. Upon receiving your instrument, please check that all items listed were shipped. If any items are missing or dam-
aged, contact your local Bio-Rad office.
3. Perform the setup installation from the checklist on the next section.

3.4 Installation Setup and Checklist of CFX96 or CFX384 System


The CFX96/CFX384 optical reaction module ships as a complete unit that is ready to setup and start. Load the
CFX96/CFX384 module on the C1000 thermal cycler chassis to set up the CFX96/CFX384 system.The
CFX96/CFX384 system should be installed on a level, clean, dry surface. Identify an appropriate work area for
the installation process prior to unpacking any system components. The entire installation process should take
approximately 15 minutes to complete. The complete system of the CFX96 Optical System is 185-5096. The
complete system of the CFX384 Optical System is 185-5034.

Note: CFX384 Optical module requires a C1000 base with 128MB RAM or higher memory.

System Checklist
___CFX96 or CFX384 Optical reaction Module.
___USB cable
___CFX Manager software installation CD
___CFX96 and CFX384 Real-Time PCR Detector instruction manual
___CFX Manager Software Installation, Protocol, Plate, Data Analysis, and Gene Expression Analysis quick
guides

___C1000 Thermal cycler base


___Power Cord
___Quick guide for the C1000 Thermal cycler
___C1000 Thermal Cycler Manual
___512 MB USB Key

Contact the local Bio-Rad office if any system components are missing or damaged.

3-2 10013582B 11/08


Installation

Using clean, dry hands, handle the CFX96 Optical Module and C1000 thermal cycler with care during unpack-
ing and assembly. Do not handle the CFX96 system components with wet hands.

1
Caution: To avoid damage to the hinge motor and lid positioning motor The CFX96 must be shipped with the
shipping screw installed, half plate in the block, lid closed and latch engaged all the way.

2
3.5 CFX96.CFX384 System Requirements

3.5.1 CFX96/CFX384 System Power and cable Requirement

3
Input power 100—240 VAC, 50—60 Hz
Indoor use Ambient temperature of 15oC—31oC. Relative

4
humidity maximum of 80% (non-condensing)
USB cable The provided USB cable is well-shielded for use with
the CFX96 system

5
3.5.2 CFX96/CFX384 PC and Software Requirement
The CFX96/CFX384 real-time PCR detection system requires CFX Manager software for instrument control
and data collection. Table 1 lists the computer system requirements for running the CFX manager software
on Windows XP and Windows Vista.

6
Table 1. Computer and Software requirements for CFX96/CFX384.
System Minimum Recommended
Operating system Windows XP Professional SP2 and Windows XP Professional SP2 and
Above or Windows Vista Home Pre- Above or Windows Vista Home Pre-

7
mium and Above mium and Above
Drive CD-ROM Drive CD-RW Drive
Hard drive 10 GB 20 GB
Processor speed 2.0 GHz 2.0 GHz

8
RAM 1 GB RAM (2GB for Windows Vista) 2 GB
Screen resolution 1024 x 768 with true-color mode 1280 x 1024 with true-color mode
USB USB 2.0, Hi-Speed port USB 2.0 Hi-Speed port
Operating system Windows XP, with Service Pack 2 Windows XP, with Service Pack 2
Internet browser
Software
Internet Explorer Internet Explorer
Microsoft Office Suite
9 10 11
Note: Running a CFX96 or CFX384 system with CFX Manager Software on a PC computer with a Windows
64-bit Operating Systems is not supported due to incompatible USB Drivers. A PC computer with a 64-bit
processor (like Intel) on a 32-bit Windows Operating System is supported.

10013582B 11/08 3-3


Installation

3.6 Setting Up the CFX96/CFX384 System


This section describes setting up the CFX96/CFX384 system.
1. CFX96/CFX384 installs similar to any of the C1000 Alpha blocks.
2. Using the hand holds on both sides, lift the CFX96/CFX384 module over the C1000 reaction module bay, and lower
it into the bay so that the Bio-Rad logo is mostly covered by the front of the module.
3. Push gently on the back of the module to move it forward until there is resistance.

Figure 3-1: CFX96/CFX384 Real Time Optical Module

3-4 10013582B 11/08


Installation

4. Pull the locking bar all the way up to lock the module into the base.

1
2
3
Figure 3-2: Place CFX96 Figure 3-3: Locking Bar in Locked Position

4
5. Check that the module is completely and evenly seated in the C1000 base.

5
6
7
8
Figure 3-4: Check for even space between module and base, as shown here.

6. No Power or communication cables are connected to CFX96/CFX384 optical module. Power and communication
with PC is provided through the C1000 thermal cycler.
7. Plug the power cord into the back of the C1000 base, and into an electrical outlet. Plug the USB 2.0 cable into the
back of the C1000, and any available computer USB 2.0 port.
9 10 11
Note: Make sure the CFX96/CFX384 is connected to a high speed 2.0 port and has Windows XP or Vista. To
check if the PC has USB 2.0, check in My Computer/Properties/Device Manager and click the Universal Serial
Bus Controllers. If Enhanced Host Controller and/or USB 2.0 Root Hub Device is listed, then the PC has USB
2.0 ports. If Universal Host Controller and/or Open Host Controller is listed, then the PC has USB 1.1 ports.

10013582B 11/08 3-5


Installation

3.7 C1000 Base RAM Memory Check


C1000 base with 128MB RAM is required for CFX384 due to the large amount of data generated by CFX384
compared to CFX96.
1. Press the F3 button under the UTILITIES on the C1000 front panel.
2. Select ABOUT under the utilities menu by pressing 1 key on the C1000 key pad.
3. Verifiy that the main PXA270 firmware version is (1.2.507.911) or above.
4. Press the F1 under MORE INFO to display the C1000 Total RAM memory and storage capacity.
5. Total amount of RAM displayed for C1000 with 128MB RAM will be 101MB or higher. This C1000 base will be
able to support CFX384 optical module.
6. Total amount of RAM displayed for C1000 with 64MB RAM will be 34MB or higher. Figure.3-5.
7. C1000 thermal cycler base with 64MB RAM should only be used with CFX96 or conventional Alpha blocks.

Figure 3-5: C1000 Memory and Storage capacity

3.8 CFX Manager Software Installation


This section describes installing the CFX Manager software from the CD provided with the CFX96 system.
CFX Manager software manages multiple instruments with combinations of reaction modules.
• Up to three S1000 thermal cyclers can be connected to a CFX96/CFX384 system.
• Up to four real time CFX96/CFX384 systems can be connected to a single PC running a single instance of
CFX Manager.

3.8.1 CFX Manager Software Installation


1. The CFX Manager software must be install on the computer by a user with administrative privileges.
2. Connect the CFX96/CFX384 via USB cable to PC.

3-6 10013582B 11/08


Installation

3. Locate the software installation disk provided with the CFX96/CFX384 System. This installation disk is compati-
ble with computers running the following operating systems: Windows XP and Vista.

1
4. Insert the CFX Manager installation CD in a CD-ROM drive.
5. If the installation program does not begin automatically, select Run… from the Start menu and then type
X:\Setup, where X is the drive letter of the CD-ROM drive. For example, if the CD-ROM is the E drive, type
E:\Setup.

2
3
4
5
6
7
Figure 3-6: CFX Manager Software

8
6. Follow all screen prompts to finalize the installation.
7.
8.
Select the default location to install the CFX Manager (C drive/Program files/ Bio-Rad/ Bio-Rad CFX).
The software will, in most cases, automatically install the necessary CFX96/CFX384 drivers.
9 10 11
9. Restart the computer before initializing the CFX96/CFX384 system for the first time.
10. If CFX96 software fails to recognize the CFX96/CFX384 Optical module, locate the driver files in the installation
CD and reinstall the driver file. Follow the direction in section 7 of this service manual to install the drivers manu-
aly.
11. The screen resolution on the PC should be set to 1024 X 768 or higher and the DPI set to Normal Size (96 DPI)
for CFX Manager software to display properly. Refer to Section 2.5 for instruction on setting up the screen resolu-
tion

10013582B 11/08 3-7


Installation

12. The driver for the CFX96/CFX384 needs to be reinstalled when a CFX96/CFX384 with a different serial number
is connected to the PC.

Note: Administrator-level privileges are required to install the software. If this is a first-time installation of the
software, the administrator must also start the application initially. Certain configurations of Windows XP And
Vista initialize new folders by assigning Read and Execute permission for the members of the ‘Users’ group. If
you have this type of operating system, and this is a first-time installation, the administrator must change the
protection on the Program Files/Bio-Rad folder so that you can save protocol, plate setup and data files. If,
after changing the protection on either of these folders, it is still not possible to write to the folders beneath
Program Files/Bio-Rad/CFX, check the Properties of each individual folder to be sure that under the Securities
tab, the box is checked that allows inheritable permissions to propagate to that folder.

3.9 System Power Up Checks


This section describes performing powering up checks.
1. Power on the system by pressing the power switch in the back panel of C1000 thermal cycler, and allow the instru-
ment to perform the power on self-test.
2. Verify proper display illumination.
3. Verify successful self-test without any fault messages.
4. Verify fan operation from the case vents.
5. Follow the instructions in the C1000 front panel to remove the shipping screw from CFX96/CFX384 inner lid. Fig-
ure: 3-7.

Figure 3-7: Instruction to remove shipping screw

6. Press the Button on the front of the CFX96/CFX384 to open the lid.

3-8 10013582B 11/08


Installation

7. Verify that the internal lid assembly moves all the way up towards the top of the instrument and moves back down to
its default location, the internal assembly should be almost even with the frame. Figure: 3-8.

1
2
3
4
5
6
7
Figure 3-8: CFX96 Lid Open

8
8. If the shipping screw is not removed using the C1000 front panel, it will be detected and can be installed and removed
using CFX Manger Software.
9. Follow the on screen direction to remove the CFX96/CFX384 shipping screw using CFX Manager.

9 10 11

10013582B 11/08 3-9


Installation

Figure 3-9: Shipping Screw Removal Screen

10. Remove the shipping screw from the heater plate in the inner lid by turning the screw one quarter turn counter clock
wise, and carefully pull it straight out of the hole. Figure 3-10.

Figure 3-10: Shipping Screw

Caution: All new CFX96 systems are shipped with the shipping screw in place. The shipping screw must be
removed prior to operating the system. Save the shipping screw for future shipping.

3-10 10013582B 11/08


Installation

Caution: The shipping screw must be installed prior to shipping the CFX96 optical module to avoid damaging
the shuttle assembly.

1
3.10 System Checkout
This section describes the checkout of the CFX96/CFX384 System.

2
1. Perform the complete Section 4 - System Checkout of this CFX96 and CFX384 Optical Module service manual.
2. Perform the complete Section 4 - System Checkout of the C1000 and S1000 thermal cycler service manual
3. Complete the CFX96/CFX384 installation report located in the Appendix section of the this service manual.

3
3.11 CFX96/CFX384 Catalog Parts and Accessories
The following parts and accessories are available from the Bio-Rad Catalog for the CFX96/CFX384 Real Time

4
System.

Catalog Number Description


184-1000 C1000 Thermal Cycler Chassis

5
184-2000 S1000 Thermal Cycler Chassis
184-0048 Dual 48/48 Fast Reaction Module
184-0096 96-Well Fast Reaction Module
184-0384 384-Well Reaction Module

6
184-5096 CFX96 Optical Reaction Module
185-5096 CFX96 Real-Time PCR Detection System
185-5034 CFX384 Real-Time PCR Detection System

7
185-1096 C1000 Thermal Cycler With 96-Well Fast Reaction Module
185-1048 C1000 Thermal Cycler With Dual 48/48 Fast Reaction Module
185-1384 C1000 Thermal Cycler With 384-Well Reaction Module
185-2096 S1000 Thermal Cycler With 96-Well Fast Reaction Module

8
185-2048 S1000 Thermal Cycler With Dual 48/48 Fast Reaction Module
185-2384 S1000 Thermal Cycler With 384-Well Reaction Module
184-5000 CFX Manager Software
184-5001
184-5005
184-5010
CFX Manager Software, Security Edition, 1 user license
CFX Manager Software, Security Edition, 5 user licenses
CFX Manager Software, Security Edition, 10 user licenses
9 10 11
184-8000 USB Cable

10013582B 11/08 3-11


Installation

Following is the recommended plastics for CFX 96/CFX384 and 1000 series instruments.

Catalog Number Description


HSP-9601 Hard-Shell® Thin-Wall 96-Well Skirted PCR Plates, clear wells, white shell, 50

HSP-9655 Hard-Shell Thin-Wall 96-Well Skirted PCR Plates, white wells, white shell, 50
HSP-3805 Hard-Shell Thin-Wall 384-Well Skirted PCR Plates, white wells, clear shell, 50
HSP-3866 Hard-Shell Thin-Wall 384-Well Skirted PCR Plates, white wells, black shell, 50
HSP-3901 Hard-Shell Thin-Wall 384-Well Skirted PCR Plates, clear wells, clear shell, 50
TLS-0801 Low-Profile 0.2 ml 8-Tube Strips Without Caps, clear, 120
TLS-0851 Low-Profile 0.2 ml 8-Tube Strips Without Caps, white, 120
TCS-0803 Optical Flat 8-Cap Strips, for 0.2 ml tubes and plates, ultraclear, 120
MLL-9601 Multiplate™ Low-Profile 96-Well Unskirted PCR Plates, clear, 25
TCS-0803 Optical Flat 8-Cap Strips, for 0.2 ml tubes and plates, ultraclear, 120
MLL-9651 Multiplate Low-Profile 96-Well Unskirted PCR Plates, white, 25
MSB-1001 Microseal® ‘B’ Adhesive Seals, optically clear, 100

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System Checkout

Section 4
System Checkout

1
4.1 About this Section

2
This section describes the procedures for the complete System Checkout of the CFX96/CFX384. System
Check out should be performed with the instrument in the fully assembled condition. All testing should be per-
formed at equilibrated room, ambient temperatures between 18 and 30 degrees C, with an ambient tempera-
ture change rate of less than 2 degrees C, per hour. All testing is to be performed with the instrument in the

3
fully assembled condition.

4
4.2 System Verification
Verification testing is the only method for determining if CFX96/CFX384 is functioning correctly and if calibra-
tion is within published specifications. Perform the tests below to verify system integrity. All testing is to be per-
formed with the instrument in the fully assembled condition. An Operational Report should be completed with

5
each system checkout. This report checklist shall provide verification that the instrument has passed the tests
in the System Checkout section. The Report is provided in the Appendix section.

6
4.3 Safety

7
Electrical
High Voltage Circuits: The 1000 series thermal Cyclers contain high voltage circuits. Instrument must have

8
power disconnected before servicing.

9 10 11

10013582B 11/08 4-1


System Checkout

Thermal
Thermally Hot Components: The Alpha block and lid heater of the 1000 series thermal Cycler can reach
temperatures of 100°C during operation of the instrument. The heated lid should remain closed at all times
during operation to prevent accidental skin burns. Always allow the Alpha block to return to its idle tempera-
ture before opening the lid and removing samples. Take caution to avoid touching the heated lid when lid
temperature control is on. When placing or removing samples, open the heated lid all the way up to allow
maximum clearance and to avoid the heated lid from falling on hands. Make sure that no object obstructs the
lid before opening it. Instrument must be allowed to cool to safe temperature before servicing.

Electro Static Discharge (ESD)


The 1000 series thermal Cycler contains ESD sensitive parts. Observe ESD precautions when handling these
parts. Wear grounding wristband and store parts in ESD shielded bags.

4.3.1 Tools and Materials


• Bio-Rad CFX Manager Software with IST test software.
• CFX96 Ultem Test Plate.
• CFX384 Ultem Test Plate
• Shuttle Pin check tool.
• Bio-Rad 96W High PCR Plate with flat caps
• Bio-Rad 96W Low PCR plate with Dome caps.
• Bio-Rad 96W Low PCR tubes with flat caps
• Bio-Rad 96W High PCR tubes with Flat caps
• Q-tips and Methanol for cleaning the Alpha block.
• Alpha Test board Fixture
• Multimeter

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System Checkout

4.4 Testing CFX96/CFX384 Alpha with Alpha Tester Board Fixture


This section tests the 1000 series alpha units using the Alpha test fixture and digital multimeter.

1
1. For accurate measurements and to avoid false readings, make sure the Alpha block is at 25°C.
2. Connect the test fixture to the connector on the alpha. Figure 4.1.
3. Use the digital multimeter to measure resistances of all test points.

2
Note: Refer to the tables for the proper test points and measured values. Tests should be performed at
ambient temperature, that is 25°C.

3
4. To test the standard Alpha units at 25°C, see the resistance tables for the desired resistance values, and the points
between which they are measured in Tables.

4
5
6
7
Figure 4-1: Alpha test Fixture

Table 1: Alpha test points and measured values


8
9 10 11
96 F as t Du al 48 /48 9 6F as t Re al 3 84 R eal
D esc rip t io n 3 84 Al p ha
Test Points Alp h a Alp h a Ti m e Ti m e

TE0 - J14 T E chan ne l 0 < 2 Oh ms <2 O h m s <2 Ohms <2 Ohms <2 Ohms
TE1- J13 T E chan ne l 1 < 2 Oh ms Open <2 Ohms <2 Ohms <2 Ohms
TE2 - J12 T E chan ne l 2 < 2 Oh ms <2 O h m s <2 Ohms <2 Ohms <2 Ohms
TE3 - J11 T E chan ne l 3 < 2 Oh ms <2 O h m s <2 Ohms <2 Ohms <2 Ohms
TE4 - J10 T E chan ne l 4 < 2 Oh ms Open <2 Ohms <2 Ohms <2 Ohms

10013582B 11/08 4-3


System Checkout

TE5 - J9 T E chan ne l 5 < 2 Ohm s <2 O h m s <2 Ohms <2 Ohms <2 Ohms
1 1- 13 1 1- 13 1 1- 13
Lid1 - J8 L i d pow er ch 1
Ohms Ohms Ohms
1 1- 13 1 1- 13 1 1- 13
Lid2 - J15 L i d pow er ch 2
Ohms Ohms Ohms
~1 0 ~1 0 ~1 0 ~1 0 ~1 0
BTS0 Block sensor 0
kOhms kOhms kOhms kOhms kOhms
~1 0 ~1 0 ~1 0 ~1 0
BTS1 Block sensor 1 o pen
kOhms kOhms kOhms kOhms
~1 0 ~1 0 ~1 0 ~1 0 ~1 0
BTS2 Block sensor 2
kOhms kOhms kOhms kOhms kOhms
~1 0 ~1 0 ~1 0 ~1 0 ~1 0
BTS3 Block sensor 3
kOhms kOhms kOhms kOhms kOhms
~1 0 ~1 0 ~1 0 ~1 0
BTS4 Block sensor 4 o pen
kOhms kOhms kOhms kOhms
~1 0 ~1 0 ~1 0 ~1 0 ~1 0
BTS5 Block sensor 5
kOhms kOhms kOhms kOhms kOhms
~1 0 ~1 0 ~1 0 ~1 0 ~1 0
HtSink(L) H ea t Sink senso r- l e ft
kOhms kOhms kOhms kOhms kOhms
H eat Sin k se nsor - ~1 0
HtSink(R) o pen o pen o pen o pe n
R ig ht kOhms
~1 0 ~1 0 ~1 0 ~1 0 ~1 0
Lid (L) Lid sensor -Left
kOhms kOhms kOhms kOhms kOhms
~1 0 ~1 0 ~1 0 ~1 0 ~1 0
Lid (R) Lid sensor -Right
kOhms kOhms kOhms kOhms kOhms
Rt_Enbl Sierra loop-back o pen o pen o pen 0 Ohm 0 Ohm
40Vsw not used
Lid Prsr not used
l_Lock Alpha loop back 0 Ohm 0 Ohm 0 Ohm 0 Ohm 0 Ohm
Table 1: Desired Resistances for 1000 series Alpha Units at 25°C

4-4 10013582B 11/08


System Checkout

4.5 C1000 Start up and Self test


This section describes the Start up self test of CFX96/CFX384 Real Time System.

1
1. Power on the C1000 cycler.
2. Verify the black boot up screen appears and a system self test is performed. Figure 4.2.

2
3
4
5
6
Figure 4-2: C1000 Black Boot Up Screen

3. Verify the second boot up screen with a moving DNA strand as shown below. Figure 4.3.

7
8
9 10 11

Figure 4-3: C1000 Boot Screen

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System Checkout

4. The main menu will appear, and System should read “IDLE” under the status bar. Figure 4.4.

Figure 4-4: C1000 Main Menu

4.6 Firmware version


This section describes the procedure to check the C1000 Firmware version,
1. Press <F1> under the Log In tab on the main menu.
2. Arrow down to highlight the Service user and select <Enter>.
3. Type the password BIORAD (in caps) using the keypad keys and select <Enter>. Figure 4.5.

Figure 4-5: Service login

4-6 10013582B 11/08


System Checkout

4. Press <F4> to return to the Main Menu screen the User name <Service> is identified in red at the top right
part of the screen under the date and time.

1
5. To Check the current versions of the C1000 firmware, Press <F3> under the Utilities tab on the main menu.
6. Press <1> on the keypad to see the About details. The PXA270, HC12, FX2, 8051 and DSP revisions are displayed.
Figure.4-6.

2
3
4
5
6
7
Figure 4-6: C1000 Firmware Version

4.7 C1000 Sensor Checker

8
The condition of all sensors and voltages of the C1000 and any connected S1000 can be viewed using the
sensor checker of C1000 Cycler.
1. Press <F1> under the Log In tab on the main menu.
2. Arrow down to highlight the Service user and select <Enter>.
3.
4.
Type the password BIORAD (in caps) using the keypad keys and select <Enter>.
Press <F4> to return to the Main Menu screen.
9 10 11
5. Press <F3> Utilities and Press < 6 > to get into service menu.
6. Press <4> Sensor Information menu.
7. The C1000 Cycler and any connected S1000 is displayed including their serial number. Figure. 4.7.

10013582B 11/08 4-7


System Checkout

Figure 4-7: Sensor Test Screen

8. Using the arrow keys highlight and select the C1000 or S1000 cycler and press <F2> Show Sensors.
9. Verify that all the sensors values and voltages of the thermal cycler is within limits. Figure.4.8.

Figure 4-8: Sensor Information Screen

4-8 10013582B 11/08


System Checkout

4.8 C1000 Diagnostic Test


The diagnostic test is included in the C1000 cyclers. The diagnostic test can be used in the service mode or

1
Administrator mode to test the functionality of the C1000 and any attached S1000.
1. Press <F1> under the Log In tab on the main menu of C1000 cycler, and log in as service user.
2. From the main menu press <F3> Utilities.

2
3. Press 6 on the key pad for the Service menu.
4. Press 3 on the key pad for Diagnostics Test.
5. Type in the name of the Operator performing the test using the keys on the keypad.
6. Verify that the name and serial number of the C1000 base and Alpha block and all attached S1000 cyclers are correct.

3
7. Press <F2> Proceed.
8. Using the arrow keys on the key pad select the desired Cycler and Press Enter Key. Letter X will be displayed next to
the selected Cycler. Figure 4.9.

4
9. Press arrow key to the right and select and place a X next to each test that needs to be performed, or press <F1> Select
All button, to select all tests and cyclers.
10. All of The diagnostic tests can be selected and run individually on any or all thermal cyclers.

5
6
7
8
9 10 11
Figure 4-9: System tests selected

11. Press <F2> Proceed.


12. The system to be tested and list of the tests to be performed will be displayed.
13. Press <F2> Start button to start the service test.
14. The screen will display the test that are being performed and prompt for user inputs on some tests. Figure 4.10.

10013582B 11/08 4-9


System Checkout

Figure 4-10: System Service Test Screen

15. Follow the prompts on the C1000 Cycler screen and continue the test until finished. The test takes about 10 - 15min.
16. Following is a brief description of the tests that will be performed.
Table 2: Diagnostic Test Description
Diagnostic Test Description
Test 1 ◊ Communications Link. Tests to see if communication is established to the C1000/
S1000 being tested. If this test fails no other tests are per-
formed.
Test 2 ◊ Interlock Check. Queries the HC12 to determine if the interlock switch is
engaged (i.e. an alpha is installed); fails if no interlock switch
is read as open.
Test 3 ◊ Alpha LED test Attempts to turn the Alpha Indicator LED on and off. The test
asks the user if the LED is on and then off and fails if the user
answers no for either case.
Test 4 ◊ Beeper Test Turns the beeper on for a short period and asks the user if the
beeper sounded. Test fails if the user answered no.
Test 5 ◊ Fans Test Turns the fans from idle to low, then medium then high speeds
asking the user if the fans turned on for all the transitions. Fails
if the user answered no to any of the questions.
Test 6 ◊ Keypad Test. Asks the user to press each key on the front panel of the C1000
or S1000 in sequence. Fails if any key press isn’t detected after
15 seconds.

4-10 10013582B 11/08


System Checkout

Diagnostic Test Description


Test 7 ◊ Sensor Integrity Test. All the sensor channels are polled for 5 seconds looking for

1
shorts or opens (readings -19.9 and less or 125 and greater).
The exception is the 3 voltage sense sensors. (40, 15 and Vcc)
These sensors are converted to their respective voltages and a
reading +- 5% fails the test.

2
Test 8 ◊Compact Flash Test Queries whether a compact flash card is present, and then
writes/reads a small file to the card. The test fails if any of
these 3 steps fail.
Test 9 ◊ Memory R/W Test Writes and reads a value to the alpha header. Test fails if

3
unable to write and read back the value from the header. Note
the test takes care to read the data that is originally at this loca-
tion in the header and restore it back after the test completes.
Test 10 ◊ Lid Heating Test Heats the lid (and also the block) to 85 degrees C. using the

4
instant incubate command. Test fails if the Lid takes more than
5 minutes to read 85 degrees or once at target the temperature
swings more than 15 degrees, or the HC12 cancels the Instant
incubate.
Test 11 ◊ Run test protocol.

5
Runs the following protocol.
METHOD BLOCK;
HOTLID 100,30;
VOLUME 0;

6
TEMP 60,45;
TEMP 90,15;
TEMP 90,15;
TEMP 30,5;

7
TEMP 95,5;
TEMP 30,5;
TEMP 90,5;
GRAD 52,60,15;

8
TEMP 4,5;
TEMP 25,5;
END
If the HC12 reports an error while running this protocol

Test 12 ◊ Raw Power TE Test.


the test fails.
Cools the Block turning each TE on in sequence, 5
9 10 11
seconds apart. The TE’s are turned on with ½ their
maximum current. Cools the block to 10 degrees. If,
after all TE’s are on, any TE that does not ramp to 10
degrees in 60 seconds will fail the test.
Test 13 ◊ System Temp Test. If any of the temperature sensors on the alpha heatsink
or main board read above 90 degrees this test will fail. It
is used after the test protocol and Raw Te Test to ensure
nothing is overheating.

10013582B 11/08 4-11


System Checkout

17. After the diagnostic test is completed a field test report is generated that lists each test performed, and if it passed or
failed.
18. The diagnostic test result will be displayed on the LCD screen.
19. To Export the diagnostic test report save the report to a thumbkey flash drive and transfer to PC.
20. Attach a thumb key flash drive to one of C1000 USB ports.
21. Select <6> Service from the Utilities menu and Press <3> on the key pad for Diagnostic Test.
22. Press <F1> View Log. A list of all diagnostic tests in memory will be displayed by serial number, date and time.
23. To view the report, highlight the test and press enter to view the test result on the C1000 LCD screen.
24. To export the test result to PC, highlight test result and press <F3> Export Log. Figure 4.14.

Figure 4-11: Diagnostic Test Export Screen

25. Export the log file to a Windows PC and print.

4.9 CFX Manager Software


CFX Manager real time software is included with a new CFX96/CFX384 system and is required for operating
the CFX96/CFX384 system. One instance of the CFX Manager can run and control up to four CFX96/CFX384
real time systems. This section describes the use of the CFX Manager to check for proper communication with
PC, removal and installation of shipping screw and firmware version of the CFX96/CFX384 system. for
detailed instruction of the CFX Manager refer to CFX96/CFX384 User manual.

4-12 10013582B 11/08


System Checkout

Note: CFX Manager software version 1.5 and above is required for support CFX384 Optical module
operation.

1
1. Install the CFX96/CFX384 on to the C1000 base Cycler.
2. Connect The CFX96/CFX384 System to PC using a shielded USB cable.
3. Power on the C1000 and allow the system to go through self test.

2
4. Launch the CFX Manager software by double clicking on the CFX Manager icon.
5. Close the Startup Wizard that launches with CFX Manger.
6. The software will detect the attached CFX systems and will display the all the system found with along with

3
their name. Figure.

4
5
6
7
8
9 10 11
Figure 4-12: CFX Manager

7. If the shipping screw is attached the following message will be displayed. Figure

10013582B 11/08 4-13


System Checkout

Figure 4-13: Shipping Screw Message Screen

8. Click OK. The instrument Properties window will open.


9. Click Remove Shipping Screw Button, then proceed to remove the shipping screw.

4-14 10013582B 11/08


System Checkout

1
2
3
4
5
6
7
Figure 4-14: Shipping Screw Removal Screen

10. Click OK Button and close the window.

8
11. Right click on the CFX systems name and select Properties from the dropdown.
12. Verify the system name, model, serial numbers and all the system firmwares are correct.

9 10 11

10013582B 11/08 4-15


System Checkout

Figure 4-15: CFX Manager Properties Screen

13. If the CFX96/CFX384 is being transported or shipped, click on the Shipping Screw tab and install the ship-
ping screw.
14. Close the Properties window and exit out of CFX Manager software.

4.10 Instrument System Test Software (IST)


This section describes the test procedure of the CFX96/CFX384 using CFX System Test Software (IST). IST
Test Software is included with Bio-Rad CFX Manager user software. CFX96/CFX384 power and communica-
tion is supplied by the CFX96/CFX384 Real Time System.

Note: CFX System Test (IST) Version 2.044 and above supports the operation of CFX384 Optical module.

1. Install the CFX96/CFX384 on to the C1000 base Cycler.


2. Connect The CFX96/CFX384 System to PC using a shielded USB cable.
3. Power on the C1000 and allow the system to go through self test.

4-16 10013582B 11/08


System Checkout

4. Verify that the latest version of the CFX manager is installed on to the PC.

Caution: The IST test software is updated upon release of new CFX/C1000 firmware files. If IST test Test ID

1
001 “Query firmware versions” fails. Then the IST test and the firmware are not compatible. The IST test
config file needs to be updated to match the firmware version. The IST config file revision in the CFXManager
might be older than the current version and needs to be updated as well.

2
5. Download the “CfxIstConfig.Xml” patch file from the CFX96/CFX384 Service CD on to the Desktop.
6. Open the CFX Manager config folder which should be located in the following location if the software was
installed in default location (C:\Program Files\Bio-Rad\CFX\Config).

3
4
5
6
7
8
Figure 4-16: CFX Manager Config folder

7. Replace the “CfxIstConfig.Xml” in the folder with the patch XMl file.
9 10 11

10013582B 11/08 4-17


System Checkout

Figure 4-17: .XML patch file

8. Close all open folders and launch the CFX System Test Software (IST) from the CFX program folder.
9. Once the Software starts it will search for the CFX96/CFX384 system. In the bottom left side of the screen it
will display “Searching for instrument”
10. When the IST establishes communication with the system it will display the serial number of the C1000 in
the bottom left corner of the screen.

4-18 10013582B 11/08


System Checkout

1
2
3
4
5
6
7
Serial number of the C1000 system found
Figure 4-18: CFX System Test

8
11. Click on Tools drop down menu, and select Bio-Rad Service login.

9 10 11

10013582B 11/08 4-19


System Checkout

Figure 4-19: Service Login

12. Password is not required for Service test. Click on the cancel button without typing anything in the box.
13. From the select test set dropdown box in the CFX System test window, select “service set”.

4-20 10013582B 11/08


System Checkout

1
2
3
4
5
6
7
Figure 4-20: IST Service Test

14. Type in operator name in the Operator ID box.


15. Enter the Ultem plate number in the Plate ID box.

8
16. The test results are saved under the serial number, date and time in a folder at the following default loca-
tion: (C;\Documents and Settings\All Users\Documents\Bio-Rad\CFX\ISTReport.
17. To change the location of where the test results are saved, click on the (...) button next to the Destination
Path box, and select the new location from the dropdown.
18. Verify that the Shipping Screw box displays “PinOut”. If the shipping screw is installed the box will display
”PinIn”. 9 10 11
19. Click on the OUT Button next to the Shipping Screw box. Remove the shipping screw and click OK.
20. Uncheck the Track box in the bottom right of the window( CFX Manager version 1.0. only).
21. All service tests are selected by default. The Individual tests can be omitted by unchecking the box next to
the test name.
22. Click on the “Execute Selected” button to run the service test.
23. The service test can not be canceled or changed when the service test is running.
24. The service tests will auto run as soon as the previous test is completed.

10013582B 11/08 4-21


System Checkout

25. The test result will be displayed in the bottom half of the window.
26. The following empty plates and tubes are required for the lid test portion of the service test (CFX96 only).
27. The plate test is ignored by software for CFX384 optical module. Unselect the plate test check boxes prior
to starting the IST test.

Test Bio-Rad
Test Name Plate/Tube Type Cap Type Bio-Rad #
ID Part #

006 Test Lid in AUTO Mode-Low plate 96W Low Plate MLL9601 Dome Cap TCS0801

010 Test Lid in Manual Mode-Low plate 96W Low Plate MLL9601 Flat Cap TCS0803

007 Test Lid in AUTO Mode-Low Tube 96W Low Tube TLS-0801 Flat Cap TCS0803

008 Test Lid in AUTO Mode-High plate 96W High plate 233-9441 Flat Cap TCS0803

011 Test Lid in Manual Mode-High plate 96W High plate 233-9441 Flat Cap TCS0803

012 Test Lid Obstruction in Manual Mode- 96W High plate 233-9441 Flat Cap TCS0803
High plate

009 Test Lid in AUTO Mode-High Tube 96W High Tube TBS-0201 Flat Cap TCS0803

28. For the low tube and high tube test place two tube strips on the opposite side of the block. Figure. 4-20.

Figure 4-21: Low and High Tube placement

29. Rotated plate Uniformity Check, requires the Ultem Plate to run. Install the plate when prompted by soft-
ware with notch of plate towards the top right corner of the block.
30. Use the Pin Check tool to check the alignment of the shuttle. Refer to section 7, alignment and calibration,
of the service manual to align the shuttle if the alignment is off.

31. Upon completion of the service test fill out the system check out report either from the test result in the bot-
tom half of the window or by opening the test result file in Excel format.

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System Checkout

1
2
3
4
5
6
Figure 4-22: IST Test Result Folder

32. Click on the Print Result button the print the to print the test result window (IST 2.044 and above only).

7
33. Complete the system check out report and attach the printed C1000 diagnostic test results and IST test
result print out.

8
4.11 IST Service Test Description
This section describes the service set tests that are performed by IST software.

001 Query Firmware versions


Make sure DSP, FX2, Front End, HC12 and Lid Firmware are current. Fail the test if this is not the case

002 Query Serial numbers


9 10 11
Make sure the Base, Block, Optical reaction module and Shuttle Serial numbers are valid. Fail the test if this is
not the case

002B Optical Head Self-Test


Run the optical head Self Test with the lid closed. Report failures if the Self Test finds errors

003 Verify block indicator


Make sure green block indicator blinks. Test fails if user does not visually confirm blinking.

10013582B 11/08 4-23


System Checkout

004 Verify Lid Open/Close using case push-button


Make sure the case opens when pressing the case push-button

005 Detect Lid Obstruction


Verify that an obstruction is properly detected by the instrument if an object is inserted and the Lid is closed.

006 Test Lid in AUTO mode - Low Plate (CFX96 only)


Make sure the Lid is properly sensing a 'Low Plate' plate in Auto mode. Low plate should return 1.

007 Test Lid in AUTO mode - Low Tube (CFX96 only)


Make sure the Lid is properly sensing a 'Low Tube' plate in Auto mode. Low tube should return 2.

008 Test Lid in AUTO mode - High Plate (CFX96 only)


Make sure the Lid is properly sensing a 'High Plate' plate in Auto mode. High plate should return 3.

009 Test Lid in AUTO mode - High Tube (CFX96 only)


Make sure the Lid is properly sensing a 'High Tube' plate in Auto mode. High tube should return 4.

010 Test Lid in Manual mode - Low Plate (CFX96 only)


Make sure the Lid is properly sensing a 'Low Plate' plate in Manual mode

011 Test Lid in Manual mode - High Plate (CFX96 only)


Make sure the Lid is properly sensing a 'High Plate' plate in Manual mode

012 Test Lid Obstruction in Manual Mode - High Plate (CFX96 only)
Verify that an obstruction is triggered by the instrument when a High Plate is inserted by the user and
the instrument is set to expect a a Low Plate in Manual Mode

015 Base unit Fans


Prompt the user to verify that the Base unit fans work when in Low, High or OFF mode.

016 Case Fans


Prompt the user to verify that the case unit fans can no longer be heard when turned OFF and working when
turned ON.
Then with the Fan control enabled in auto mode, a check is performed to make sure the ambient temperature
stays within acceptable range for about 3 minutes.

019 Check Pin


Prompt user to confirm that the 'Check Pin' fixture can be inserted in Well E7 after the shuttle is moved to a
special position

025 Rotated Plate Uniformity plate


Use CFX96 or CFX384 Ultem uniformity plate to verify that each well give consistent result

026 Scan with Lid Open.


Open the CFX lid turn on the Leds, scan through all 96 wells. Do a fast fly over with blue Led on only.

027-Reference Row Check (no plate required)


Take a plate read with no plate and compare the reference row to the factory calibrated reference row.

4-24 10013582B 11/08


System Checkout

Report error if the two rows compared are too far apart.

028C Bare block scan for contamination (Normal)

1
Verify that the block is clean. Report to user wells that are found contaminated.

029 Base Unit Self-Test


Run the Base Unit (Thermal Cycler) Self-Test and report errors if any are found

2
030 Optical Head check
Same as Test 002B performed a second time

3
031 Shuttle Slots Valid
Verify that the shuttle has the right number of factory and user calibrated slots

032 Shuttle Slots Valid


Verify that the shuttle has valid factory calibrated slots

4
033 Verify Lid Open/Close using motorized commands
Open and close the lid using the motorized commands to verify it works as expected

5
040 Verify Block performance
Make sure the Base Unit can drive the block to different temperatures.

041 Verify Lid Heating

6
Make sure the Lid can be driven to different temperatures

042 Verify Shuttle Heating


Make sure the shuttle temperature can be maintained to 45C for several minutes

7
050 Verify Shuttle EEPROM
Verify that the Shuttle EEPROM is valid

051 System EEPROM

8
Capture critical data from the EEPROM

9 10 11

10013582B 11/08 4-25


Preventative Maintenance

Section 5
Preventative Maintenance

1
5.1 Introduction

2
This section provides information on the preventative maintenance procedure for the CFX96/CFX384 and
C1000 Thermal Cycler. The CFX96/CFX384 optical module and C1000 thermal cyclers requires little mainte-
nance to maintain proper operation and precise thermal control. However, the CFX96/CFX384 optical reaction
module should be cleaned, along with the C1000 thermal cycler base, on a regular schedule to remove any

3
debris or dirt that might interfere with proper function. Cleaning the instrument allows precise
instrument function. Preventative Maintenance (PM) is recommended once a year.

5.2 Tools and Materials

4
• Small Hand Tools
• Cleaning Materials:
• IPA (Rubbing Alcohol)

5
• Cotton swabs (Q-Tip)
• Soapy water (Liquid dishwashing agent)
• Soft cloth

6
5.3 Preventative Maintenance

5.3.1 PM of CFX96 Reaction Module

7
1. Unplug power cable from the C1000 thermal cylcer to prevent electrical shock.
2. To clean spills off the outside case, use a damp cloth or tissue. If needed, use a mild soap solution, and then rinse
the surface with a damp cloth. Cleaning the cover will prevent corrosion.

8
Warning: Never use cleaning solutions that are corrosive to aluminium. Never clean the block with strong
alkaline solutions (strong soap, ammonia, or high-concentration bleach). Never use corrosive or abrasive
cleaning solutions. These cleaning agents can damage the block and prevent precise thermal control. Avoid
scratching the surface of the bay. Scratches and damage to this surface interfere with precise thermal control.

3. Remove the CFX96/CFX384 cover.


9 10 11
4. Inspect and clean the reference spots on the inside of lid cover plate.
5. Inspect and clean dust and debris from the CFX96/CFX384 housing.
6. To Clean the cooling fins of CFX96/CFX384, Remove dust with a damp cloth. Remove any heavy dust that is deep
in the vents with a vacuum cleaner. Use water and a soft, lint-free cloth to remove debris that is stuck to the fins.

Caution: Use of mineral oil or any other oil is not recommended on the CFX96/CFX384 Alpha.

10013582B 11/08 5-1


Preventative Maintenance

7. If oil is used on the Alpha block wells, use a solution of 95% ethanol to clean oil. Do not allow oil to build up in the
block.
8. Visually inspect sample block wells for dirt or residue spills. Clean as required with IPA and cotton swabs.
9. Allow the reaction block to thoroughly dry prior to heating the block.
10. To clean the inner lid, use a soft, lint-free cloth and water to remove debris and solutions from the inner lid surface.
Never use abrasive detergents or rough material that will scratch the surface. Cleaning the inner lid improves pre-
cise sample heating and cooling.
11. Reassemble the instrument.

5.3.2 PM of C1000 Thermal Cycler Chassis


1. Unplug the thermal cylcer to prevent electrical shock.
2. Remove top cover.
3. Visually inspect for dirt or dust buildup around fans. Clean as required with soapy water and soft cloth.
4. Reassemble instrument.

Caution: Use of abrasive detergents or rough material will scratch the control panel.

Warning: Never use cleaning solutions that are corrosive to aluminium. Never clean the block with strong
alkaline solutions (strong soap, ammonia, or high-concentration bleach). Never use corrosive or abrasive
cleaning solutions. These cleaning agents can damage the block and prevent precise thermal control. Avoid
scratching the surface of the bay. Scratches and damage to this surface interfere with precise thermal control.

5.3.3 Maintaining Sufficient air flow

The C1000 thermal cycler requires sufficient air flow to heat and cool precisely. If the flow of air is blocked
the thermal cycler cannot ramp to the correct temperature in the specified time.

1. Provide enough space around the C1000 thermal cycler and between adjacent instruments for sufficient air flow.
2. If more than one Cycler is on the bench, arrange instruments so that the warm exhaust air from one instrument does
not enter the air intake vents of another.
3. Shield the thermal cycler from heat sources, such as radiators, other heat producing instruments, and bright sun-
light.
4. If the air temperature is above 31¤C at the front air intake vents of C1000, adjust the air conditioning to lower the
ambient temperature.

5.3.4 Perform System Checkout


1. Perform the System Checkout section of this Service Manual.
2. Fill out the CFX96/CFX384 Preventive maintenance report.

5-2 10013582B 11/08


Preventative Maintenance

1
CFX96 Real-Time System
Preventative Maintenance Report

2
Customer: Case Number:
Performed by: Serial #: Date:

3
Component Checked Replaced Cleaned
Chassis Inspection
Power-On Test

4
Clean Reference Spots
Housing Cleaned
Inner Lid
Communication

5
CFX96 Real Time Alpha Block
Keypad
Display Function

6
System Checkout

Comments:

7
The CFX96 real time system has been serviced for preventative maintenance and meets all of the PM require-
ments for the CFX96 Real Time System.

8
Performed by____________________________________________ Date__________________________
Bio-Rad Service Engineer

9 10 11

10013582B 11/08 5-3


Preventative Maintenance

CFX384 Real-Time System


Preventative Maintenance Report
Customer: Case Number:
Performed by: Serial #: Date:

Component Checked Replaced Cleaned


Chassis Inspection
Power-On Test
Clean Reference Spots
Housing Cleaned
Inner Lid
Communication
CFX384 Real Time Alpha Block
Keypad
Display Function
System Checkout

Comments:

The CFX384 real time system has been serviced for preventative maintenance and meets all of the PM
requirements for the CFX384 Real Time System.

Performed by____________________________________________ Date__________________________


Bio-Rad Service Engineer

5-4 10013582B 11/08


Removal and Replacement

Section 6
Removal and Replacement

1
6.1 Introduction

2
This section of the manual provides instructions on the proper way to remove and replace parts and assem-
blies. Alignment procedures that should be performed when an assembly is replaced, are listed in this section
in the Replacement / Adjustment Matrix. The procedures indicated should be performed in the order they are
listed in the matrix.

3
Note: Removal and replacement procedures which are obvious from the appearance of the unit are not
included. Unless otherwise specified, following the removal instructions in reverse order will provide the
correct procedure for replacing the assembly.

4
6.2 Replacement / Adjustment Matrix
The following table shows what adjustment or checkout procedures must be performed after an assembly is

5
replaced. The calibration procedures must be performed even if the original assembly is being reinstalled in the
same unit. They must be performed in the order specified.

R ep la cea b le As sy. Ad ju st m en t / C ali b rat io n S ect i on

6
M ain Bo ar d P ro gr am ser i al nu mbe r S ectio n 7
M ain Bo ar d R un Syst em Ch ecko ut S ectio n 4
M ai n Bo ar d S ec ti o n 7

7
6.3 Removal and Replacement Procedures

8
6.3.1 Tools Required

Allen Wrench Set


Nut Driver Set
Wire cutter
9 10 11
Screwdrivers Set - Phillips and Flat Tip
Tie Wraps - Size Small and Medium

10013582B 11/08 6-1


Removal and Replacement

6.4 Removing the CFX96/384 Housing Cover


This section will describe the removal of CFX housing cover.
1. Install CFX on to the C1000 base, and power on the system.
2. Press the front close/open button on the front of the CFX to open the CFX optical module.
3. Power off the system and remove the CFX from the C1000 base.
4. Remove two screws from the back of the housing and loosen the two screws from the front inside of the cover. Figure
6-1 and 6-2.

Figure 6-1: Housing back cover screws Figure 6-2: Housing cover screws

5. Partial remove the cover and disconnect the LED cable before removing the cover completely.

6.5 Remove the Upper FCC Board and Cable Assembly


This section will describe the removal of the FCC board assy.
1. Remove the two screws that mounts the upper board on to the frame. Figure 6-3.
2. Unplug the upper board from the main board and disconnect Y-axis stepper motor cable, Y-axis micro switch cable
and Y-home sensor cable cables from the board. Figure 6-4.

6-2 10013582B 11/08


Removal and Replacement

1
2
3
4
Figure 6-3: FCC Upper board Screws Figure 6-4: Disconnect FCC Upper board

5
Note: Do not disconnect the flex cables. The flex cables and the boards come as a set.

3. Carefully place the board on the top of the frame housing. Make sure not to bend or put too much strain on the Flex

6
cable.
4. Remove two screws from the X-axis board. Unplug the X-axis motor cable, X-axis limit switch and X-home sensor
cable from the board. Figure 6-5 and 6-6.

7
8
9 10 11

10013582B 11/08 6-3


Removal and Replacement

Figure 6-5: FCC X-axis board Figure 6-6: FCC X- axis board screw removal

5. Remove two screws that holds the board on to the shuttle assembly and disconnect the board from the shuttle assem-
bly. Figure 6-7 and 6-8.

Figure 6-7: FCC Shuttle Board screws Figure 6-8: FCC Shuttle board removal

6. Remove the FCC upper board assembly carefully as not to damage or strain the flex cable connecting the three
boards. see Figure 6-9.

Note: FCC board assembly comes as a set and needs to be replaced as a set. see Figure

6-4 10013582B 11/08


Removal and Replacement

Figure 6-9: FCC Upper Board Assembly

6.6 Removing the Main Board

1
This section will describe the removal of CFX main board.

2
Note: Prior to removing the main board save calibration data using FX2 service software (section 7 of this
service manual)

1. Remove the housing cover and remove the screws from the upper FCC board and unplug the FCC board from the
main board.

3
2. Remove four screws and the shield from the back of main board. Figure 6-10 and 6-11.

4
5
6
Figure 6-10: Main Board Shield Figure 6-11: Main Board

7
3. Unplug eleven sensor and motor cables from the upper right corner of the main board.

8
9 10 11

Figure 6-12: Sensor and Motor Connectors Figure 6-13: Main Board Connectors

10013582B 11/08 6-5


Removal and Replacement

Caution: Use a flat tip screw driver to wedge the connectors from the main board to dislodge the connectors.
Do not pull on the cable to disconnect them from the main board. The main board connectors are very delicate
and can be damaged easily!

4. The main board is held on to the frame by two snap mounts. Carefully remove the board from the snap mounts to get
access to the lid heater and power cables located on lower inside of main board.
5. Unplug the lid heater cable from the bottom side of main board by pulling up the tabs on the both sides of connector
to unlock and remove the lid heater cable. Figure 6-14 and 6-15.

Figure 6-14: Lid Heater and Switch Pod Cable Figure 6-15: Power Cable

6. Unplug the switch pod cable and main power harness cable from the main board, and remove the main board.
7. Install new main board. Use FX2 service software to write the previously saved calibration data back on to the main
board.

6.6.1 Installing New Main Board


1. Use the FX2 service software to set the main board to either CFX96 or CFX384.
2. Use FX2 service software to restore the main board data, if the original main board data were saved prior to
removal.
3. Upon installation of new main board, Reference spots data needs to be re-calibrated using the manufacturing IST
test no 21.
4. Start the IST system software and from the Tools menu select Bio-Rad Service Login.
5. Service login password is “Sierra94547”.
6. Enter the operator name and start the Factory set of the IST test.
7. Individual tests of Factory set of the IST are not selectable, there for run Factory set test 001 through 021(6 Chan-
nels Step and Repeat).
8. Click on Cancel button to cancel the Factory IST test after test 21 (6 Channels Step and Repeat) is completed.

6-6 10013582B 11/08


Removal and Replacement

6.7 Removing the CFX Real Time Alpha


This section will describe the removal of the real time Alpha from CFX Optical module.

1
1. Place the CFX on its side.
2. Remove the four screws that holds the Alpha on to the CFX. Figure 6-16.

2
3
4
5
Figure 6-16: Alpha Screw Removal Figure 6-17: Unplug Power and LED Cables

6
3. Unplug the power harness cable and LED extender cable from the Alpha. Figure 6-17.
4. Remove the Alpha.

Note: Refer to Section 7 of this service manual to convert a conventional CFX96 alpha to real time CFX96

7
alpha if real time alpha is not available

6.8 Base Plate Overlay

8
1. Peel off the old Base plate overlay and clean leftover adhesive from the base plate.
2. Remove the protective paper from the new Base plate overlay, align and attach the overlay on the base plate. Figure
6-18.

9 10 11

10013582B 11/08 6-7


Removal and Replacement

Figure 6-18:

6.9 Removing the XY stage assembly.


This section will describe the removal of the XY stage assembly. CFX96 XY stage is different than the CFX384
XY Stage and are not interchangeable.
1. Remove the main board and FCC board assembly.
2. Unplug all cables and connections of XYstage.

Note: All cables and connections must be unplug before removing the XY assembly from the housing.

3. Remove three snap rivets from the right and left Apron and remove both aprons. Figure 6-19 and 6-20.

6-8 10013582B 11/08


Removal and Replacement

1
2
3
4
Figure 6-19: Snap Rivet Figure 6-20: left and Right apron Removal

4. Remove the four screws, washers and springs that mounts the XY stage to the top frame. Figure 6-21.
5. From the right side of the CFX upper frame, remove the screw and spring that holds the XY stage to the gear box.

5
Figure 6-22.

6
7
8
9 10 11
Figure 6-21: XY Stage Screws Figure 6-22: Gear Box Screw

Caution: Hold one hand under the XY stage to prevent it from falling out of the frame.

6. Carefully lower and remove the XY stage making sure not to damage the pulleys and rails. Figure 6-23.

10013582B 11/08 6-9


Removal and Replacement

Figure 6-23: XY Stage Removal Figure 6-24: XY Stage Assembly

6.10 Reference Spots Removal


1. Remove the lid heater and strain relief bracket. Don’t unplug the Lid heater from the main board.
2. Remove the four screws that holds the lid heater pad to the XY Stage and remove the lid heater pad.
3. Remove the reference spots and replace with correct reference spot.
4. Install the lid heater pad alignment pins and install the lid heater pad.

6-10 10013582B 11/08


Removal and Replacement

1
2
3
4
5
6
5. Install the lid heater assembly.

6.11 Front Motor Removal

7
1. Remove the housing cover.
2. Unplug the front motor from the main board.
3. loosen the motor clamp screw.

8
9 10 11

10013582B 11/08 6-11


Removal and Replacement

4. Carefully remove the motor from the clamp.

6.12 Front Motor Assembly Removal


This section will describe the removal of the front motor assembly.
1. Remove the upper FCC board and XY Stage.
2. Remove four screws that mounts the Motor Assembly to the CFX frame.
3. Remove four locknuts that mounts the upper frame to the frame housing and remove the upper frame.

4. Unplug the two limit sensor cable and front motor cable from the main board.
5. Remove the front motor assembly.

6-12 10013582B 11/08


Removal and Replacement

1
2
3
4
5
Note: Note The location of the O ring on the assembly, it comes off very easily!

6.13 Lid Position Sensor

6
1. Remove the two screws and disconnect connector at the main board.
2. Mark the position of the sensor before removing it. The position of this sensor determines the correct amount of pres-
sure applied on the PCR plate. (Figure 6-41)

7
8
9 10 11

10013582B 11/08 6-13


Removal and Replacement

Caution: Mark the position of the current location of the sensor. Position of this sensor is critical to the
function of the lid pressure.

6.14 Lid Position Gear Box


1. Remove the housing cover and upper FCC board.
2. Unplug the lid position Motor cable and Lid position sensor from the main board.
3. Remove the screw and spring that mounts the XY stage to the lid position gear box from the right side of the upper
frame.
4. Remove four locknuts that mounts the upper frame to the frame housing.
5. Remove one screw from each side of the upper frame that mounts the gear box to the upper frame.

6.15 Hinge Motor Removal


1. Loosen the hinge motor clamp screw.
2. Unplug the motor cable from the main board.
3. Pull the motor carefully out and make sure not to damage the motor encoder.

6-14 10013582B 11/08


Removal and Replacement

1
2
3
4
6.16 Hinge Assembly Removal

5
This section will describe the separation of the optical module and the base assy.
1. Remove the upper FCC board and main board.
2. Remove the XY stage.

6
3. Remove the hinge motor.
4. Remove the two screws that mounts the hinge support pinion to the right side bracket of the CFX frame and remove
the support pinion, teflon washer and the two bearings. Figure

7
8
9 10 11

5. Remove the two screws that attaches the left side of the frame to the left bracket. Figure.
6. Remove two locknuts that mounts the left frame bracket to the top back frame. Figure.
7. Remove three screws that mounts the hinge gear to the right frame bracket. Figure.

10013582B 11/08 6-15


Removal and Replacement

8. Open the lid and use a flat tip screwdriver and wedge it between the gear and the base and gently press until the shaft
(Figure 6-25)and the key bearing on the other side (Figure 6-26) of the hinge is displaced.

6-16 10013582B 11/08


Removal and Replacement

9. Thread hinge rode torsion out of the left frame bracket and bearing. Figure.

1
2
3
4
5
6
10. Remove one screw from the bottom and two screws from the top of the right frame bracket that attaches it to the CFX
frame. Figure.

7
11. Remove the right bracket and thread the hinge assembly out of the CFX frame. Figure.

8
9 10 11

10013582B 11/08 6-17


Removal and Replacement

Note: When separating the Optical Module and the base plate, be careful not to damage any connectors that
are present.

12. Re-install new Hinge assembly in reverse order.


13. To properly align the hinge motor assembly, loosen the two hinge support pinion screws.
14. Place the Hinge Alignment Tool into the hinge clamp and verify that the tip of the tool is all the way in the support
pinion bracket. Figure.

6-18 10013582B 11/08


Removal and Replacement

1
2
3
4
15. While holding the tool in place by hand, tighten the hinge motor clamp screw until the tool doesn't turn.

5
16. Tighten the two hinge support pinion bracket screws.

6
7
8
9 10 11
17. Loosen the motor clamp screw and remove the alignment tool.
18. Install the hinge motor and tighten the motor clamp screw. Figure
19. Verify that the CFX lid moves up and down easily

10013582B 11/08 6-19


Removal and Replacement

6.17 CFX96 Lid Heater Assembly


1. Remove four screws to the rubber baffle skirt (Figure 6-50)
2. Remove two screws from the strain relief bracket and remove the strain relief. (Figure 6-51)

6-20 10013582B 11/08


Removal and Replacement

3. Remove four screws from plate heater cover . (Figure 6-52)

1
2
3
4
4. Remove four screws from the main board but do not remove the board.

5
5. Move the main board out to get access to the lid heater cable.

Note: Do not remove any of the connectors on the main board! Remove only the four screws! This is
to provide clearance to the lid heater flex cable on the main board to be removed!

6
6. To remove the flex cable use a flat tip screwdriver and gently pull on the sides of the connector to release the flex
cable and pull the cable from connector.
7. Remove the lid heater and heater plate cover. Figure

7
8. Remove the plate detector flag from the old heater plate. Figure

8
9 10 11

10013582B 11/08 6-21


Removal and Replacement

9. Verify that the tab on the flag is bent up 1.0mm to 1.5mm at the tip of the tab.
10. Install the flag on the new lid heater plate. Make sure it is centered in the heater plate hole and is moving freely and
spring biased to the plate. Figure

11. Use lid position alignment tool to align and install the new lid heater.

6.17.1 Plate Flag Verification


Follow the steps below to verify that the plate flag has been adjusted correctly.
1. Install the CFX96 on to the C1000 base and power on the system.
2. After the CFX96 completed its self test, press the lid button to open the lid and remove any plates or tubes from the
block.

6-22 10013582B 11/08


Removal and Replacement

3. Close the lid and re-open it again. When the lid opens all the way, the inner lid plate assembly should start to move
inside the CFX96 housing momentarily (away from user) and then back out (towards the user). It should stop when
it is approximately even with the outer lid housing. This is the homing process at power-up condition.

1
4. Place a 96 well hard-shell low plate (Bio-Rad part# HSP9665) w/o any caps or sealing film in the block,
and close the lid.
5. Open the CFX96 lid by pressing the open/close button.

2
6. Once the lid is open the inner lid plate assembly should NOT move toward the user.

Note: The CFX96 lid default setting is low plate. The inner lid plate assembly will not have to adjust and move
up or down when a low plate is detected.

3
7. Next remove the plate and close the unit with the open/close button.
8. Open the unit with the open/close button. Once the unit is fully open the inner lid plate assembly should now
move towards the user. This confirms that it can sense tubes.

4
9. Plate verification is complete. Power off the unit

6.18 CFX384 Lid Heater Removal

5
1. Remove four screws from the main board but do not remove the board.
2. Move the main board out to get access to the lid heater cable.

Note: Do not remove any of the connectors on the main board! Remove only the four screws! This is

6
to provide clearance to the lid heater flex cable on the main board to be removed!

3. To remove the flex cable use a flat tip screwdriver and gently pull on the sides of the connector to release the flex
cable and pull the cable from connector.

7
4. Remove two screws from the strain relief and remove the strain relief. Figure
5. Remove four screws from the lid heater plate. Figure

8
9 10 11

10013582B 11/08 6-23


Removal and Replacement

6. Remove the lid heater and heater plate cover.

7. Use 384 lid position alignment tool to align and install the new lid heater.

6-24 10013582B 11/08


Adjustment and Calibration

Section 7CFX96/CFX384
Adjustment and Calibration

1
7.1 Introduction

2
This section of the manual provides instructions for adjusting, calibrating, and maintaining the CFX96/CFX384
optical module for Adjustment and calibration of the CFX96/CFX384 Real Time System refer to the C1000 and
S1000 thermal cycler service manual 10010296. Each procedure also has a short introduction explaining its
purpose.

3
7.2 Safety
Hazardous voltages and hot surfaces are present inside the thermal cycler. Care should be exercised to pre-
vent injury whenever the cover is removed. The procedures in this section should be performed by qualified

4
technicians only.

7.3 Test Equipment

5
• USB Cable
• USB Thumbkey
• CFX System test software(IST)/CFX Manager.
• Fx2_USB test and calibration utility.

6
• Pin Check Tool
• Lid Alignment Tool
• Ultem plate

7
7.4 Fx2 USB Test and Calibration Utility
Fx2 USB test and calibration utility is used to calibrate X Y position, program serial number, model type, save

8
and restore main board data align shuttle position, align shipping screw position and test the CFX96/CFX384
system. This section details the service menu items of Fx2 USB Utility software.

9 10 11

10013582B 11/08 7-1


Adjustment and Calibration

Figure 7-1: FX2 USB Main Menu Screen


1. Double click on the “fx2_usb_test.exe” to start the software.
2. The software will start and search for any connected C1000 cycler.
3. Once the C1000 unit is detected the software will display the message “ Found Bio-Rad C1000”.

7-2 10013582B 11/08


Adjustment and Calibration

1
2
3
4
5
6
7
Figure 7-2: C1000 instrument Detected
4. Click Ok. The main menu screen will be displayed.

8
9 10 11

10013582B 11/08 7-3


Adjustment and Calibration

7.4.1 Service Menu


The fx2_usb_test program service menu can be selected by either pressing the “s” key on the key board, or
double clicking on the service menu.

Figure 7-3: Service Menu

Caution: All menus of FX2 USB other than service is intended for R&D use. Use of these menus and
commands can overwrite important calibration manufacturing data which can damage the instrument beyond
repair and void the warranty of the CFX96/CFX384.

7-4 10013582B 11/08


Adjustment and Calibration

The Service menu of Fx2 USB Utility has following items:

• a. Save Main board data

1
• b. Confirm and ReStore Main Board Data
• c. ReConnect to USB Device
• d. Read Alpha Block Type
• e. Program Alpha Block to Real Time Block
• f. Display Sierra Instrument Type

2
• g. Program Sierra Instrument type
• h. Do POST and Display Result
• i. Move shuttle(CH0) to a specified well
• j. Turn ON specified Channel LED
• k. Turn OFF all LEDs

3
• l. Move to Shipping Screw Position
• m. Set Shipping Screw Flag
• n. Clear Shipping Screw Flag
• o. Get shipping flag Status

4
• p. Write Sierra Serial Number
• q. Display Sierra Serial Number
• r. Display Shuttle Serial Number
• s. Display All Faults Info
• t. Clear All Faults

5
• u. Home X Axis Motor
• v. Home Y Axis Motor
• w. Display stored X start Y start Xlockdownoffset and Ylockdownoffset
• y. Execute stop and read scan
• z. Execute flyover

6
• 1. XY Stage ReCalibration Sub Menu

7
8
9 10 11

10013582B 11/08 7-5


Adjustment and Calibration

7.4.2 Save Main board data


This menu item is used to read the calibration data from the old (original) main board of the Sierra unit and
the data will be stored in a file.

Figure 7-4: Save Main Board Data

Whenever Sierra Main board is replaced, all the calibration data stored on the old main board needs to be
transferred to new sierra main board. Also the Sierra Serial number and the Sierra Instrument type needs to
be restored. If the calibration data can not be read from old main board, Service set of CFX managers
System test software (IST) test needs to be run to calibrate the new main board.

Following data item are stored:


• Sierra Serial Number
• Sierra Instrument Type
• X Start and Y Start position
• Shipping PIN position (X LockdownOffset, Y LockdownOffset)
• Ref Row factory Data
• Ref row factory date and time
• Extra Cal Data storage Area

7-6 10013582B 11/08


Adjustment and Calibration

7.4.3 Confirm and ReStore Main Board Data


This menu item is used to write the stored calibration data to the new (replaced) main board. Some of the

1
data (like Sierra Serial number, Sierra Instrument type, X Start and Y Start) will be displayed on the screen
and after the confirmation from the user, calibration data will be restored to the new main board of the Sierra
unit.

2
3
4
5
6
7
8
Figure 7-5: Restore Main Board Data Screen

7.4.4 ReConnect to USB Device 9 10 11


This menu item is used to reconnect Everett/Sierra unit. Without restarting the test program, communication
can be established to new Everett/Sierra unit or after restarting existing Sierra unit.

After the calibration data stored from the old main board, Sierra power is turned OFF. The main board is
replaced by the new main board, and Sierra power is turned back ON. To start communication with Sierra
unit again, we use this menu item to reconnect USB device, without closing the test program.

10013582B 11/08 7-7


Adjustment and Calibration

7.4.5 Read Alpha Block Type


This menu item is used to read Alpha block type. Selecting this menu item will display whether the Alpha
Block is 96 W or 384 Well and also display whether it is conventional or real time block.

7.4.6 Program Alpha Block to Real Time Block


This menu item is used to program the alpha block to Real time Alpha Block from Non real time (conven-
tional) Alpha Block for 96 Well and 384 Well. Selecting this item will ask user input for Alpha Block Type (0
for 96 Well Real time and 1 for 384 Well Real time block).

Caution: Once a conventional Alpha block is programed to a real time Alpha Block block, it can not be repro-
grammed back to a conventional Alpha block

Figure 7-6: Alpha block Programming Screen

7-8 10013582B 11/08


Adjustment and Calibration

7.4.7 Display Sierra Instrument Type


This menu item is used to display the Sierra Instrument type. Selecting this menu item will display whether

1
the Sierra is 96 Well or 384 Well instrument.

7.4.8 Program Sierra Instrument type

2
This menu item is used to program the Sierra Instrument and Alpha type (96 Well or 384 Well). Selecting
this item will ask user input for Instrument type (0 for 96 Well and 1 for 384 Well Sierra).

7.4.9 Do POST and Display Result

3
This menu item is used to do POST (Power On Self Test) and will display the POST results. During POST,
Sierra firmware moves Shuttle to X and Y limits and checks for limit switches and also reads reference well
spot data, it also checks CPLD, RAM and Flash memory. The POST results will be interpreted and appro-
priate descriptive results will be displayed. If no faults detected the message will display “Post completed
Fault Count; )”.

4
5
6
7
8
9 10 11

10013582B 11/08 7-9


Adjustment and Calibration

7.4.10 Move shuttle to a specified well


This menu item is used to move the shuttle to specified well by specifying Row and Column information.
User need to input Row and Column value. Accepted Row value for 96 Well instrument is 0 to 7 and for 384
Well instrument 0 to 15. Row A= 0. Accepted Column value for 96 Well instrument is 0 to 11 and for 384 Well
instrument 0 to 2
1. Press “i” button on the keyboard.
2. Type in the Row number that the shuttle needs to move to in the box and press OK button.

Figure 7-7: Move Shuttle to a Specific Row

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Adjustment and Calibration

3. Type the Column number to move to in the box and press enter. The shuttle will move to that Row and Column.

1
2
3
4
5
6
7
Figure 7-8: Move the Shuttle to Specific Column

8
9 10 11

10013582B 11/08 7-11


Adjustment and Calibration

7.4.11 Turn ON specified Channel LED


This menu item is used to turn ON specified channel LED. This will cause the selected channel LED to blink
continuously. Select numbers 0-5 for all six Leds. Refer to the figure bellow for Led locations and numbers to
turn on the led. Figure

3 0 2

5 1 4

Figure 7-9: Led locations and Numbers

7.4.12 Turn OFF all LEDs


This menu item is used to turn OFF all LEDs.

7.4.13 Move to Shipping Screw Position


This menu item is used to move to Shipping Screw position.

7.4.14 Set Shipping Screw Flag


This menu item is used to set Shipping Screw flag in the Sierra firmware. If this flag is set in the firmware,
firmware will not allow to do any scan. Normally this flag is set, when a Shipping Screw is placed in position.

7.4.15 Clear Shipping Screw Flag


This menu item is used to clear Shipping Screw flag in the Sierra firmware. Normally this flag is cleared,
when a Shipping Screw is removed from a Sierra unit.

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Adjustment and Calibration

7.4.16 Get shipping flag Status


This menu item is used to display current status of Shipping Screw flag in the firmware. Display of 1 indi-

1
cates that the Shipping Screw flag is set and display of 0 indicates that the Shipping Screw flag is clear.

2
3
4
5
6
7
8
Figure 7-10: Shipping Screw Flag Status

7.4.17 Write Sierra Serial Number


This menu item is used to write Sierra Serial number on Sierra Main Board. 9 10 11

10013582B 11/08 7-13


Adjustment and Calibration

7.4.18 Display Sierra(CFX) Serial Number


This menu item is used to display Sierra Unit Serial Number.

Figure 7-11: Display Sierra Serial number

7.4.19 Display Shuttle Serial Number


This menu item is used to display Shuttle Serial Number.

7.4.20 Display All Faults Info


This menu item is used to display current faults information of the Sierra unit.

7.4.21 Clear All Faults


This menu item is used to clear all the current faults information logged in the Sierra unit firmware.

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Adjustment and Calibration

7.4.22 Home X Axis Motor


This command will move the X axis motor to home position.

1
7.4.23 Home Y Axis Motor
This command will move the Y axis motor to home position.

2
7.4.24 Display Stored X start Y start X lockdownoffset and Y lockdwonoffset
This menu item will display the stored X and Y start values for the shuttle position and X lockdownoffset and
Y lockdown offset for the shipping screw position that was programed at the factory.

3
Caution: Always record these stored values prior to servicing the CFX96/CFX384. Incase the stored values
are erased and the shuttle and shipping screw positions needed to be restored.

4
5
6
7
8
9 10 11

Figure 7-12: Stored X and Y Start Values

10013582B 11/08 7-15


Adjustment and Calibration

7.4.25 Set New X start Y start X lockdownoffset and Y lockdwonoffset


This menu command is used to set new shuttle X and Y start values and shipping screw X and Y values on
to the main board. After all the values are typed in verify that the correct values are stored by selecting the
Display Stored Xstart ystart command.

7.4.26 Execute Stop and Read Scan


Selecting this command will turn on the Leds and scan across 96 well plate. This command is used to
quickly verify that all the Leds are functional.
1. Press the open/close button on the CFX to Open the CFX96/CFX384 Lid.
2. Press “y” on the key board to Execute the stop and read scan command.
3. Enter “63” in the box for channels to eliminate. 63 will turn on all six Leds during the plate read Scan.

Figure 7-13: Stop and Read Scan


4. All six LEDs should turn on and the shuttle should scan through the 96 well from the bottom up.

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Adjustment and Calibration

5. Upon successful completion return value of 1 will be displayed. Figure

1
2
3
4
5
6
7
Figure 7-14: Scan Return Value Screen

8
7.4.27 Execute Flyover
Selecting this menu command will turn on either channel 0 or 1 Led and will do a fast fly over the block.
1. Press the open/close button on the CFX to Open the CFX96/CFX384 Lid.
2. Press “z” on the key board to select the Execute Fly over command.
9 10 11
3. In the Channel select box enter 0 or 1 for the Led channel to turn on.
4. Press OK button. The Led channel will turn on and the shuttle will perform a quick fly over the complete block from
the bottom up.
5. Upon successful completion return value of 1 will be displayed.

10013582B 11/08 7-17


Adjustment and Calibration

7.4.28 XY Stage ReCalibration Sub Menu


Selecting this sub menu takes us to another menu for doing XY stage re-calibration. Recalibration of the X
and Y start position may be necessary if the stored values couldn’t be retrieved from the main board or
manufacturing.

The XY stage re-calibration sub menu has following menu items:


• a. Display stored X Start, Y Start, X lockdownoffset and Y Lockdownoffset values
• b. Move shuttle to the PIN CHECK position
• c. Move Shuttle by one microstep in +X direction
• d. Move Shuttle by one microstep in -X direction
• e. Move Shuttle by one microstep in +Y direction
• f. Move Shuttle by one microstep in -Y direction
• g. Move Shuttle by ten microstep in +X direction
• h. Move Shuttle by ten microstep in -X direction
• i. Move Shuttle by ten microstep in +Y direction
• j. Move Shuttle by ten microstep in -Y direction
• k. Display, confirm and write new X Start and Y Start values
• l. Move shuttle to the Shipping Screw position
• m. Display, confirm and write new X lockdownoffset and Y Lockdownoffset values

For the XY stage re-calibration, we first need to move the shuttle to PIN CHECK position, then visually check
to see in which direction we need to move shuttle, so that PIN CHECK position aligns properly. Once shuttle
aligns properly at PIN CHECK position, then we need to write new values of XSTART and YSTART into
Sierra main board.

Next, we need to move the shuttle to SHIPPING SCREW position and visually inspect to see in which direc-
tion (in X axis) we need to move shuttle, to align SHIPPING SCREW position properly. At the end of align-
ment we need to write new SHIPPING SCREW position (X lockdownoffset and Y Lockdownoffset) on the
Sierra main board.

7.4.28.1 Display current X Start, Y Start, X and Y lockdownoffset values


This menu item is used to display current values of X Start, Y Start, X lockdownoffset and Y Lock-
downoffset. Selecting this menu item reads these values from Sierra instrument and display these values.

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Adjustment and Calibration

1
2
3
4
5
6
7
Figure 7-15: Display the X and Y stored values

8
7.4.28.2 Move shuttle to the PIN CHECK position
This menu item is used to move the Shuttle to PIN CHECK position. When this item is selected, test soft-
ware, sends command to Sierra firmware to move the Shuttle to PIN CHECK position. Test software also
reads X Start and Y Start values from the Sierra firmware. Next when, shuttle is moved by one microsteps
in +X, -X, +Y or -Y direction using menu items c, d, e, or f, test software will track these motion and will
adjust X Start and Y Start values. 9 10 11

10013582B 11/08 7-19


Adjustment and Calibration

7.4.28.3 Move Shuttle by one or ten microstep in +X direction


This menu item is used to move the Shuttle by one or ten microstep in +X direction. Depending on,
whether the Shuttle is at PIN CHECK position or at Shipping Screw position, this motion adjust X Start or
X LockDownOffset value respectively.

Figure 7-16: Move the Shuttle in X direction by one Microstep Screen


7.4.28.4 Move Shuttle by one or ten microstep in -X direction
This menu item is used to move the Shuttle by one or ten microstep in -X direction. Depending on,
whether the Shuttle is at PIN CHECK position or at Shipping Screw position, this motion adjust X Start or
X LockDownOffset value respectively.

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Adjustment and Calibration

7.4.28.5 Move Shuttle by one or ten microstep in +Y direction


This menu item is used to move the Shuttle by one or ten microstep in +Y direction. When the Shuttle is

1
moved by selecting this menu item, the Y Start value is adjusted, when shuttle is at PIN CHECK position.

2
3
4
5
6
7
8
Figure 7-17: Move the Shuttle By ten Microstep
If the shuttle is at the Shipping Screw position, the shuttle motion using this menu item will not change Y
Start or Y LockDownOffset. Y LockDownOffset value is always fixed compared to Y Start value.
9 10 11
7.4.28.6 Move Shuttle by one or ten microstep in -Y direction
This menu item is used to move the Shuttle by one or ten microstep in -Y direction. When the Shuttle is
moved by selecting this menu item, the Y Start value is adjusted, when shuttle is at PIN CHECK position.

If the shuttle is at the Shipping Screw position, the shuttle motion using this menu item will not change Y
Start or Y LockDownOffset. Y LockDownOffset value is always fixed compared to Y Start value.

10013582B 11/08 7-21


Adjustment and Calibration

7.4.28.7 Display, confirm and write new X Start and Y Start values
This menu item is used to display the new values of X Start and Y Start. User message will be displayed to
check that Shuttle is at the PIN CHECK position. If user click on YES, then test software will write these
new values of X Start and Y Start to the Sierra instrument.

Figure 7-18: Display and Write New Xstart and Ystart Values
7.4.28.8 Move shuttle to the Shipping Screw position
This menu item is used to move the Shuttle to Shipping Screw position. When this item is selected, test
software, sends command to Sierra firmware to move the Shuttle to Shipping Screw position. Test soft-
ware also reads X LockDownOffset and Y LockDownOffset values from the Sierra firmware. Next when,
shuttle is moved by one microsteps in +X, or -X direction using menu items c, or d test software will track
these motion and will adjust X LockDownOffset value. ALso test software will check value of Y Lock-
DownOffset and if it is not correct, it will write correct value to the Sierra Instrument.

7-22 10013582B 11/08


Adjustment and Calibration

7.4.28.9 Display, confirm and write new X and Y lockdownoffset


This menu item is used to display the new values of X lockdownoffset and Y Lockdownoffset. User

1
message will be displayed to check that Shuttle is at the Shipping Screw position. If user click on YES,
then test software will write these new values of X lockdownoffset and Y Lockdownoffset to the Sierra
instrument.

Figure 7-19: Display and Write New Shipping Screw position


2
3
4
5
6
7
8
9 10 11

10013582B 11/08 7-23


Adjustment and Calibration

7.5 CFX96/CFX384 Firmware Upgrade


This section of the manual provides instruction on how to update the firmware contained in the CFX 96 instru-
ment. The CFX 96 instrument consists of the C1000 thermal cycler base unit coupled with the 96 well Optical
Reaction Module containing a total of five user accessible firmware installations.

C1000 Base Firmware File Name Rename File to


HC12 EV0100XYZ00.ABS.S19 UPDATE.S19
PXA270 NK.1.X.Y.Z.BIN NKUPDATE.BIN
FX2 FX2_SAT_BULK.DLD
CFX96 Optical Module File Name Rename File to
Firmware
DSP OPTHEADLP1.DLD
8051 SLIDMAIN.DLD

7.6 C1000 and CFX96/CFX384 Firmware Upgrade Procedure


1. Power up the C1000 instrument.
2. When the C1000 has fully booted and is in the Main Menu form, log in as follows:
3. Press the Log In (F1) softkey.

7-24 10013582B 11/08


Adjustment and Calibration

4. Select ADMIN user, press Enter. The cursor will move to the Password field. Leave the password field blank and press
Enter a second time.

1
5. Current User in the title bar of the form will indicate ADMIN.
6. Return to the Main Menu form by pressing the Main Menu (F4) softkey.
7. Open the Utilities form by pressing the Utilities (F3) softkey.
8. Open the Administrator Settings menu by pressing the "5" key.

2
9. Open the Update System menu by pressing the "7" key.
10. From the Update System menu select the firmware option to be updated and proceed to the following instructions.

3
7.6.1 Update C1000 PXA270 Firmware
PXA270 Firmware resides in the front end board of C1000 thermal cycler. PXA270 includes the Windows
CE, The C1000 control Gui, Satellite S1000 communication and PC services.
1. Insert the thumb drive, with the necessary update files installed, into an available USB port.

4
2. From the Update Menu, select option 2 "PXA270 Updater" and press Enter.
3. The Update form will appear with the currently installed version displayed.
4. When ready, press Enter. The system will scan the thumb drive for the necessary file (NKUPDATE.BIN). If found,

5
the system will copy the update file to memory and then scan the file. When done, both the current and update ver-
sions will be displayed.
5. Press Enter to start the update process. Do Not turn off power or remove any devices during this process. The sys-
tem will erase the old image from flash memory and then program the new image into flash memory. This process
will take 2 - 3 minutes to complete.

6
6. When the update has completed the system will indicate "Update Complete! Please Reboot ALL Systems." Power
off the instrument, then power it back on.
7. Go to the Utilities form by pressing the Utilities (F3) softkey and select the About option. Verify that the "Firmware

7
Version" is correct.

7.6.2 Update C1000 HC12 Firmware


HC12 firmware resides on the main board of C1000 and S1000 Thermal Cyclers and is responsible for

8
thermal control of C1000 and S1000.
1. Insert the thumb drive, with the necessary update files installed, into an available USB port.
2. From the Update Menu, select option 1 "HC12 Updater" and press Enter.
1. The Update form will appear with all attached devices shown.
2. The form will appear with all attached devices enabled for Update. If any are to be excluded from the update, press
the softkey under the desired device to Toggle it to the "Don't Update" state.
9 10 11
3. When ready, press Enter. The system will scan the thumb drive for the necessary file (UPDATE.S19). If found, the
message "Please press ENTER to begin update" will be presented. Press Enter.
4. The update process will start. Do Not turn off power or remove any devices during this process. The progress bar
will indicate the state of the update. This process will take 1 - 2 minutes to complete.
5. When the update has completed the system will indicate "Update Complete! Please Reboot ALL Systems." Power
off all instruments, then power them back on.
6. Go to the Utilities form by pressing the Utilities (F3) softkey and select the About option. Verify that the "HC12"
firmware version is correct.

10013582B 11/08 7-25


Adjustment and Calibration

7.6.3 Update C1000 FX2 Firmware


FX2 is the USB control firmware of the C1000 and S1000 and resides on the main board of the C1000/
S1000 Thermal cycler.
1. Insert the thumb drive, with the necessary update files installed, into an available USB port.
2. From the Update Menu, select option 3 "FX2 Updater" and press Enter.
3. The Update form will appear with all attached devices shown.
4. The form will appear with all attached devices enabled for Update. Do Not update more than one at a time. Press the
softkey under all but one of the devices to Toggle them to the "Don't Update" state.
5. When ready, press Enter. The system will scan the thumb drive for the necessary file (FX2_SAT_BULD.DLD). If
found, the message "Please press ENTER to upgrade" will be presented. Press Enter.
6. The update process will start. Do Not turn off power or remove any devices during this process. This process will
take 1 - 2 minutes to complete.
7. When the update has completed the system will indicate "Update Complete! Please Reboot ALL Systems." Power
off all instruments, then power them back on.
8. Go to the Utilities form by pressing the Utilities (F3) softkey and select the About option. Verify that the "FX2"
firmware version is correct.

7.6.4 Update CFX 96/CFX384 DSP Firmware


DSP firmware is in the main board of the CFX96/CFX384. DSP is responsible for data acquisition and
control of the shuttle LEDs and photo diodes.
1. Insert the thumb drive, with the necessary update files installed, into an available USB port.
2. From the Update Menu, select option 4 "DSP Updater" and press Enter.
3. The Update form will appear with the currently installed version displayed.
4. When ready, press Enter. The system will scan the thumb drive for the necessary file (OPTHEADLP1.DLD). If
found, the system will display the update version.
5. Press Enter to start the update process. Do Not turn off power or remove any devices during this process. This pro-
cess will take 1 - 2 minutes to complete.
6. When the update has completed the system will indicate "Update Complete! Please Reboot ALL Systems." Power
off the instrument, then power it back on.
7. Go to the Utilities form by pressing the Utilities (F3) softkey and select the About option. Verify that the "DSP" Ver-
sion is correct.

7.6.5 Update CFX 96/CFX384 8051 SmartLid Firmware


8051 smart lid firmware resides on the CFX96/CFX384 main board and is responsible for the smart lid
control.
1. Insert the thumb drive, with the necessary update files installed, into an available USB port.
2. From the Update Menu, select option 5 "8051 Updater" and press Enter.
3. The Update form will appear with the currently installed version displayed.
4. When ready, press Enter. The system will scan the thumb drive for the necessary file (SLIDMAIN.DLD). If found,
the system will display the update version.

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Adjustment and Calibration

5. Press Enter to start the update process. Do Not turn off power or remove any devices during this process. This pro-
cess will take 1 - 2 minutes to complete.

1
6. When the update has completed the system will indicate "Update Complete! Please Reboot ALL Systems." Power
off the instrument, then power it back on.
7. Go to the Utilities form by pressing the Utilities (F3) softkey and select the About option. Verify that the "8051"
Version is correct.

2
3
4
5
6
7
8
7.7 Installing the Drivers Manually
If needed, install the drivers manually by following these instructions:
1. Insert the software CD. If the CD is not available, then locate the drivers folder in the file path C:\Program Files\Bio-
Rad\Drivers on your hard drive.
2. Click the Drivers button software installation screen.
9 10 11
Click the BaseUnit folder to open it.

10013582B 11/08 7-27


Adjustment and Calibration

Figure 7-20: Base Unit Folder

3. For Windows XP computers, double-click BioRadC1000DriverInstall.exe to launch the installation window. For
Windows Vista, right-click BioRadC1000DriverInstall.exe and select Run as Admin to launch the installation win-
dow.

Figure 7-21: Driver Installation Screen

7.8 System Messages Log


Before starting a new run, each instrument initiates a self-diagnostic test to verify that it is running within specifications.
The software records results of this test in the Messages log. To view the messages log or save it to thumb drive.
1. Login to the C1000 as Admin or Service.
2. Put in a USB thumbscrew on the USB port of the C1000 cycler.
3. Press F3 button under Utilities.
4. Press 4 button on the keypad for system Messages Log.
5. Scroll down to view the log files.
6. Press F3 under export file to export the log file on to the USB thumb drive.

7-28 10013582B 11/08


Adjustment and Calibration

1
2
3
4
5
Figure 7-22: System Messages Log

7.9 Power Failure Option

6
In a power failure, the instrument and computer will shut down. If the power failure is short, then the instrument will
resume running a protocol, but the Application log will note the power failure. Depending on the length of time that the
power is off and the computer settings, the instrument and software attempt to continue running depending on the protocol
step:

7
• If the protocol is in a step with no plate read, then the protocol continues running as soon as the instrument gets
power again
• If the protocol is in a step with a plate read, then the instrument waits for the software to restart and resume
communication to collect the data. In this situation, the protocol only continues if the software is not shut down
by the computer. When the computer and software start up again, then the protocol continues

8
If you experience an extended power failure, you might want to open a motorized lid on a reaction module to remove your
samples. Follow these steps to manually open the module by removing the locking plate:
1. Remove the reaction module from the C1000 chassis.
2. Position the module on the front of a desk, so that the front of the module extends 2 inches over the edge of the desk.
3. With a screw driver, remove the two large screws from the under the front edge of the reaction module (below the but-
ton for opening the lid). Do not remove the two small screws that are located at the front edge of the module. You
9 10 11
should hear the locking latch release from inside the module. This image shows the two large screws.

10013582B 11/08 7-29


Adjustment and Calibration

Figure 7-23: Locking latch Removal

4. Push the reaction module lid open. Notice that the latch (dark plastic) is no longer attached.
5. Reassemble the reaction module with the lid open by replacing the locking latch and securing it with the large screws.

Figure 7-24: Locking Latch in place

7.10 Converting Conventional Alpha to Real-time Alpha Block


This section describes the procedure to convert a conventional 96 well block to a real time 96 well Alpha block.
1. De-solder the SMT Led located in corner of the Alpha block board marked D3.

7-30 10013582B 11/08


Adjustment and Calibration

1
2
3
4
5
Figure 7-25: Alpha D3 Led Location

6
2. Install the Alpha O-Ring on to the Alpha block. Use a small amount of instant loctite to hold the O-Ring in place. Loc-
tite 495 is used at manufacturing).

7
8
9 10 11
Figure 7-26: Alpha O-Ring Installation
3. Install alpha jumper on position J4 of the Alpha Block board.

10013582B 11/08 7-31


Adjustment and Calibration

Figure 7-27: Mini Jumper to J4 on Alpha Board

4. Attach the Alpha to the CFX96/CFX384 and connect all cables.


5. Place the CFX96/CFX384 on to C1000 Base and connect to PC via USB cable.
6. Power on the C1000 and start the Fx2_USB utility software.
7. From the service menu select Program Alpha Block to Real Time Block.
8. Select Display Alpha block type to verify the Alpha is programed to real time Alpha block.

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Troubleshooting

Section 8
Troubleshooting

1
8.1 Introduction

2
The troubleshooting information in this section will help to identify and diagnose operating difficulties and
component failures in the CFX96/CFX384 System. This section may be expanded to include additional trou-
bleshooting aids as service center experience identifies recurrent problems and appropriate diagnostic
processes.

3
If after reading through this manual, you find that you need additional assistance in resolving a problem, you
may contact our Technical Service Department by phone at 800-424-6723, or by FAX at 510-741-5802.

8.2 Troubleshooting the CFX96/CFX384 System

4
This section provides troubleshooting information in three parts. The first part lists Error Messages, followed by
symptoms and probable causes. The second part is a list of error codes and descriptions. The third part is a
troubleshooting guide that uses a Problem, Cause, Solution format for determining the root cause of problems.

8.2.1 Error Messages

5
Error Messages Cause Solution
SELF-TEST FAILED ON X If selftest fails the user will see that it A user can power cycle and see if

6
failed on the MAIN menu error persists; A user can run self-
test from the TOOLS menu.
BLOCK OVERHEATED. POWER Reaction module has exceeded maxi- Wait for block to cool down. If the
INSTRUMENT OFF THEN BACK ON. IF mum temperature of 107.5˚C or sen- error message persists, the sensor on

7
ERROR PERSISTS, CONTACT BIO-RAD sor has a malfunction and is not the Block or the C1000 main board is
TECHNICAL SUPPORT. measuring temperature accurately. bad.
Protocol terminated.
HEATSINK OVERHEATED. POWER Heatsink temperature has exceeded Wait for HS to cool down. If the error

8
INSTRUMENT OFF THEN BACK ON. IF 75˚C. Protocol terminated. message persists, the sensor on the
ERROR PERSISTS, CONTACT BIO-RAD Block or the C1000 main board is
TECHNICAL SUPPORT. bad.

SYSTEM OVERHEATED. POWER


INSTRUMENT OFF THEN BACK ON.
ERROR PERSISTS, CONTACT BIO-RAD
IF
Amplifier 1 temperature has
exceeded 85˚C. Protocol terminated.
Wait for amplifier to cool down.If the
error message persists, the C1000
main board is bad.
9 10 11
TECHNICAL SUPPORT.

ALL BLOCK SENSORS FAILED. CON- All block sensors have failed (see You can recycle power and see if this
TACT BIO-RAD TECHNICAL SUPPORT. below for failure criteria). Protocol was a fluke, If the error message per-
terminated. sists, the Block or the C1000 main
board is bad.

10013582B 11/08 8-1


Troubleshooting

Error Messages Cause Solution


POWER SUPPLY OVERHEATED. CON- Power Supply temperature has Wait for PS to cool down, If the error
TACT BIO-RAD TECHNICAL SUPPORT. exceeded 85˚C. Protocol terminated. message persists, the C1000 main
board is bad.

PROTOCOL CANCELLED DUE TO Lid sensor has failed during lid pre- User may try to re-run or power cycle
HEATED LID FAILURECONTACT BIO- heat. Protocol terminated. to see if error goes away. If the error
RAD TECHNICAL SUPPORT. message persists, the Lid heater is
bad.

SYSTEM OVERHEATING. PLEASE Amp temp has exceeded 80˚C. Sys- Wait for amplifier to cool down.
CHECK AIRFLOW. IF ERROR PERSISTS, tem beeps and displays error. install the latest HC12 Firmware.
CONTACT BIO-RAD TECHNICAL SUP- Check the C1000 Fan operation
PORT.

SLOW BLOCK CYCLING. CONTACT Block failed to achieve target in the Block may be slow, but protocol still
BIO-RAD TECHNICAL SUPPORT. estimated time. may be successful. Defective Block
or C1000 main board
SLOW LID CYCLING. CONTACT BIO- Lid failed to achieve target in the Lid may be slow, but protocol still
RAD TECHNICAL SUPPORT. estimated time. may be successful. Defective Lid
heater or C1000 main board
SLOW GRADIENT CYCLING. CON- Block failed to achieve gradient in Block may be slow, but protocol still
TACT BIO-RAD TECHNICAL SUPPORT. the estimated time. may be successful. Defective Block
or C1000 main board
HEATED LID FAILED. CONTACT BIO- (singles only) If the right and left lid Power must be cycled, the block is
RAD TECHNICAL SUPPORT. heater channels deviate from each now at 4˚C and the only way out of
other by more than 5˚C, the protocol this error condition is a power cycle.
is terminated and the block sent to 4C
Defective Block or C1000 main
to preserve samples
board.
BLOCK SENSOR 0 - 5 FAILED. CON- One of the six block sensors 0 - 5 has Power must be cycled, the block is
TACT BIO-RAD TECHNICAL SUPPORT. failed and the protocol was termi- now at 4C and the only way out of
nated. this error condition is a power cycle.
Defective Block or C1000 main-
board.
LEFT / RIGHT LID SENSOR FAILED. Left/ Right lid sensor has failed. If a (single) power must be cycled, the
CONTACT BIO-RAD TECHNICAL SUP- dual, protocol terminated. If a single block is now at 4C and the only way
PORT. and BOTH lid sensors failed, proto- out of this error condition is a power
col terminated and block sent to 4°C. cycle.
Defective Block or C1000 main
board.
LID OVERHEATED AND WAS SHUT (duals only) Lid has overheated and Lid has severely overheated. User
OFF. CONTACT BIO-RAD TECHNICAL has been shut off and protocol has could wait for lid to cool down and
SUPPORT. been terminated. try again, but for the overtemp sensor
to trip, it is most likely a run-away lid
PROTOCOL CANCELLED DUE TO Power / Logic to block is out of Run the C1000 sensor checker and
BLOCK / LOGIC POWER FAILURE. range. observe the power supply voltages.
CONTACT BIO-RAD TECHNICAL SUP-
PORT.

8-2 10013582B 11/08


Troubleshooting

Error Messages Cause Solution


PROTOCOL CANCELLED DUE TO MISS- Reaction module has been removed. Put block or CFX96 back in

1
ING BLOCK. CONTACT BIO-RAD Protocol terminated.
TECHNICAL SUPPORT.
MEMORY CORRUPT, PROTOCOLS MAY Protocol storage memory has been S1000; Perform a full reset
BE LOST. CONTACT BIO-RAD TECH- corrupted. C1000: Perform a full reset of the
NICAL SUPPORT. HC12 and a system restore from the

2
C1000 to restore factory protocols.
BAD REACTION MODULE. PLEASE Unable to read information from Unplugged USB cable, None CFX96
POWER INSTRUMENT OFF AND THEN reaction module properly. Real Time Alpha Block, Defective
BACK ON. IF ERROR PERSISTS, CON- Block.

3
TACT BIO-RAD TECHNICAL SUPPORT.

INCORRECT CHECKSUM. PLEASE Information read from reaction mod- None CFX96 Real Time Alpha
POWER INSTRUMENT OFF AND THEN ule appears incorrect. Block, Defective Block.
BACK ON. IF ERROR PERSISTS, CON-

4
TACT BIO-RAD TECHNICAL SUPPORT.
PROTOCOL CANCELLED DUE TO One of the block sensors in a single Cycling power is the only way to
BLOCK SENSOR FAILURE AT CYCLE X, block has failed. The system has “clear” this error condition. Defec-
STEP Y. PLEASE POWER INSTRUMENT cancelled the protocol at step x, cycle tive Block or C1000 Main board.
OFF AND THEN BACK ON. IF ERROR y and sent the block to 4C to preserve

5
PERSISTS, CONTACT BIO-RAD TECH- the samples.
NICAL SUPPORT.

FLASH MEMORY ERASE FAILED. OHFD_FLASH_ERASE_TIMEOU Cycle power and reload firmware
PLEASE RETRY OPERATION. IF ERROR T: Primarily results from attempt to

6
PERSISTS, CONTACT BIO-RAD TECH- upgrade while instrument is in fault
NICAL SUPPORT. state. The failure would be reported
directly by API call in this case. If
occurred during run represents seri-
ous hardware fault.

7
CALIBRATION UPDATE FAILED. OHFD_ROM_DATA_UPDATE_FAI If recurrent bad main board or C1000
PLEASE CONTACT BIO-RAD TECHNI- L: Should never occur in normal cus- front end board
CAL SUPPORT. tomer use. If occurs during field ser-
vice calibration updates, retry
operation.

8
FLASH MEMORY ERASE FAILED. OHFD_ROM_DATA_ERASE_FAIL On repeated failure, Replace the
PLEASE RETRY OPERATION. IF ERROR : Primarily results from attempt to main board
PERSISTS, CONTACT BIO-RAD TECH- upgrade while instrument is in fault
NICAL SUPPORT. state. The failure would be reported
directly by API call in this case. If
occurred during run represents seri-
ous hardware fault.
9 10 11
FLASH MEMORY ERASE FAILED. OHFD_ROM_KEY_ERASE_FAIL: On repeated failure, Replace the
PLEASE RETRY OPERATION. IF ERROR Primarily results from attempt to main board
PERSISTS, CONTACT BIO-RAD TECH- upgrade while instrument is in fault
NICAL SUPPORT. state. The failure would be reported
directly by API call in this case. If
occurred during run represents seri-
ous hardware fault.

10013582B 11/08 8-3


Troubleshooting

Error Messages Cause Solution


CALIBRATION DATA IS INVALID. OHFD_ROM_DATA_KEY_ERROR Attempt reload of factory calibration
PLEASE POWER INSTRUMENT OFF : ROM calibration data is invalid. data and retry. On recurrence,
THEN BACK ON. IF ERROR PERSISTS, Replace main board.
CONTACT BIO-RAD TECHNICAL SUP-
PORT.
HEAD POSITIONING FAILURE. IF OHFD_STEPPER_MOVE_TIMEO Check for loose screws or parts on
ERROR PERSISTS, PLEASE CONTACT UT: DSP board hardware failure. the X Y stage. Possible bad main
BIO-RAD TECHNICAL SUPPORT. Will have produced fault state. Diag- board or FFC board Assy.
nostic use only.
POSITION SENSOR FAILURE. IF ERROR OHFD_HOME_NEGLIM_STUCK: Check for loose screws, limit
PERSISTS, PLEASE CONTACT BIO-RAD Negative limit remained tripped after switches or parts on the X Y stage.
TECHNICAL SUPPORT. backoff move. Possibly stuck mecha- Possible bad Limit switch or FFC
nism or problem with stepper drive board Assy.
or connection.

POSITIONER HOMING ERROR. PLEASE OHFD_NO_HOME_DETECTED: Check for loose screws, limit
POWER INSTRUMENT OFF THEN BACK Possibly stuck mechanism or prob- switches, Sensors or other parts on
ON. IF ERROR PERSISTS, PLEASE CON- lem with stepper drive or connection. the X Y stage. Possible bad Limit
TACT BIO-RAD TECHNICAL SUPPORT. Obstruction to head motion. switch or FFC board Assy.
POWER-ON TEST FAILED: ROM Bad Sensor, limit switch, loose parts Test all switches and sensors, thigh-
ERROR. IF ERROR PERSISTS, CON- or bad FFC or main board ten and align loose screws and parts.
TACT BIO-RAD TECHNICAL SUPPORT. Replace bad board
SHUTTLE TEMPERATURE IS HIGH. OHFD_SHTL_TEMP_ABOVE_60C Bad cooling fan, fan connector, temp
PLEASE POWER INSTRUMENT OFF : Shuttle temperature is above 60 sensor or main board.
THEN BACK ON. IF ERROR PERSISTS, degrees C. Operation halted.
CONTACT BIO-RAD TECHNICAL SUP-
PORT.

LID FAILED TO UNLOCK. POWER Front Mot/Cam opening Error. This Check for loose screws and parts on
INSTRUMENT OFF THEN BACK ON. IF error can happen due to: 1. Motor is the X Y stage and front motor assem-
ERROR PERSISTS, CONTACT BIO-RAD stuck. 2. Encoder of motor is not bly. test front motor and sensors.
TECHNICAL SUPPORT. working. 3. Motor is not getting
power. 4. Connection to motor is bro-
ken.
LID FAILED TO LOCK. PLEASE CHECK Front Motor/Cam Closing Error. This Hinge Sensor defective. Check for
FOR OBSTRUCTION. IF NONE, POWER error can happen due to: 1. Motor is loose screws and parts on the X Y
INSTRUMENT OFF THEN BACK ON. IF stuck. 2. Encoder of motor is not stage and front motor assembly. test
ERROR PERSISTS, CONTACT BIO-RAD working. 3. Motor is not getting front motor and sensors.
TECHNICAL SUPPORT. power. 4. Connection to motor is bro-
ken. 5. Obstruction
LID FAILED TO OPEN. PLEASE CHECK Hinge Motor Opening Error. There Test Hinge motor, hinge limit sensor.
FOR OBSTRUCTION. IF NONE, POWER might be obstruction on the way, Check hinge assembly for loose or
INSTRUMENT OFF THEN BACK ON. IF which might not allow the motor to broken parts.
ERROR PERSISTS, CONTACT BIO-RAD open the Lid or it can be due to motor
TECHNICAL SUPPORT. hardware failure.

8-4 10013582B 11/08


Troubleshooting

Error Messages Cause Solution


LID FAILED TO CLOSE. PLEASE Hinge Motor Closing Error. There Hinge Sensor defective. Check for

1
CHECK FOR OBSTRUCTION. IF NONE, might be obstruction on the way, loose screws and parts on the X Y
POWER INSTRUMENT OFF THEN BACK which might not allow the motor to stage and front motor assembly. test
ON. IF ERROR PERSISTS, CONTACT close the Lid or it can be due to front motor and sensors.
BIO-RAD TECHNICAL SUPPORT. motor hardware failure.

2
Lid Close detect Switch Error. This
error can happen due to: 1. Lid close
detect switch is not working properly.
2. Connection to switch is broken. 3.
Very thin obstruction is present,

3
which allows cam to start locking,
but lid can not close fully.
LID POSITIONING ERROR. PLEASE Positioner Homing Error. This error Test the Hinge motor and all sensors.
POWER INSTRUMENT OFF THEN BACK can happen due to: 1. Motor is stuck. Hinge Sensor defective. Check for
ON. IF ERROR PERSISTS, CONTACT 2. Encoder of motor is not working. loose screws and parts on the X Y

4
BIO-RAD TECHNICAL SUPPORT. 3. Motor is not getting power. 4. Con- stage and front motor assembly. test
nection to motor is broken. 5. Posi- front motor and sensors.
tioner home flag is not working/set
properly.

5
LID OBSTRUCTION. PLEASE REMOVE Obstruction Error. This error occurs Check the front motor limit sensors
OBSTRUCTION AND CLOSE THE LID. IF due to obstruction on the way of lid and gear box sensor
ERROR PERSISTS, CONTACT BIO-RAD closing, or using plate/tube with
TECHNICAL SUPPORT. wrong height.
LID FAILED TO LOCK/UNLOCK. One or both (Open/Close Sensor) Check for loose parts. Test all sensors

6
POWER INSTRUMENT OFF THEN BACK Front mot/cam Sensor Error. This and motors.
ON. IF ERROR PERSISTS, CONTACT Error occurs due to: 1.one or both
BIO-RAD TECHNICAL SUPPORT. (Open/Close Sensor) Front mot/cam
Sensor malfunctioning. 2. Dust or

7
some scraping on the surface of sen-
sor. 3. Connector/wire broken.
LID FAILED TO OPEN/CLOSE. PLEASE One or both (Open/Close Sensor) Check for loose parts. Test all sensors
CHECK FOR OBSTRUCTION. IF NONE, Hinge mot Sensor Error. This Error and motors.
POWER INSTRUMENT OFF THEN BACK occurs due to: 1.one or both (Open/

8
ON. IF ERROR PERSISTS, CONTACT Close Sensor) Hinge Sensor mal-
BIO-RAD TECHNICAL SUPPORT. functioning. 2. Dust or some scraping
on the surface of sensor. 3. Connec-
tor/wire broken. 4. Obstruction

8.2.2 Error Codes


9 10 11
Error Message Description
Communications error. This error message is displayed when communications with
a previously good connection is no longer working.
USB connection error Universal Serial Bus (USB) handle is used to communicate
with an attached device. This error message is displayed
when a previous good USB handle is determined to be
invalid. This may be the results of the device being discon-
nected or power to the device was interrupted or lost.

10013582B 11/08 8-5


Troubleshooting

Error Message Description


File IO error. This message is displayed when the software tries to read/
write a file. This is mainly a diagnostic message for during
development of the software but could possible occur in a
release.
Operation not supported. This message is displayed when a command is sent to a
device that is not supported. An example might be an open
lid command to a device that has no lid.
A unexpected exception has Exception - any occurrence of an abnormal condition that
occurred. causes an interruption in normal program execution.
Start run failed. This message is displayed when a run (protocol) is started
but fails to start.
Communication error. Internal This error message is displayed when during the instrument
satellite ID for C1000 not found. discover phase the software determines that an C1000
instrument has no internal satellite ID. The command
"DEVICES?" returns a list of ID's, each of these ID's repre-
sents an attached S1000 device attached to the C1000
device. There should always be at least one ID returned by
the "DEVICES?" command.
Duplicate base serial number. This error message is displayed when during the instrument
discover phase the software determines that more than one
attached instrument has the same base serial number.
Duplicate block serial number. This error message is displayed when during the instrument
discover phase the software determines that more than one
attached instrument has the same block serial number.
Reaction block missing or may This message is displayed when the software determines
not be seated properly. Check that the reaction block is missing. The software determines
that the locking bar is pulled all this by sending the RCI command "BLOCKCOUNT?" to
the way up and that the block is each attached device.
pushed forward.
Protocol run prevented due to no 40V to Sierra turned off.
power to optical head. Please
power instrument off then back
on. If error persists, contact Bio-
Rad Technical Support.
Protocol run did not start. This message is displayed when a protocol run does not
start after 60 seconds.
Device busy This message is displayed when a protocol run is attempted
on a device that is currently running a protocol.
Shipping pin installed. Shipping This message is displayed when a protocol run is attempted
pin must be remove before a pro- and the shipping pin is installed.
tocol run can be started.
Calibration failed. This message is displayed when a calibration run has failed.
Run report file IO error. This message is displayed when the writing of the run report
has failed.
Preheating time out. This message is displayed when preheating the lid and shut-
tle takes longer than 10 minutes.

8-6 10013582B 11/08


Troubleshooting

Error Message Description


Duplicate satellite ID. This message is displayed when the software determines

1
that the same satellite ID is used mote than once. During the
discover phase the RCI command "DEVICES?" returns a
list of ID's, one for each attached S1000 connected to a
C1000. The list of ID's contains the same ID more than
once.

2
Warning ambient temperature This message is displayed when the upper board ambient
has exceeded 50 degrees centi- temperature is greater than 50 degrees centigrade.
grade. If ambient temperature
exceeds 60 degrees centigrade,

3
any running protocol is can-
celled and power to the optical
head is turned off.
Warning ambient temperature This message is displayed when the upper board ambient
has exceeded 60 degrees centi- temperature is greater than 60 degrees centigrade. When

4
grade. Any running protocol is ambient temperature is greater than 60 digress the 40V to
cancelled and power to the opti- optical head is turned off and any protocol running is can-
cal head is turned off. celed.
Satellite/PC service log size to This message is displayed when the satellite/PCservice logs

5
big. are greater than 50 mega bytes.
Existing plate read file overwrit- This message is displayed when an existing plate read file is
ten. being over written.
Running on A: PROTOCOL Displayed when a machine running a protocol has

6
NAME POWER OUTAGE been turned off, either intentionally or due to a
DURING power outage, and then turned on again.
CYCLE X STEP Y
RESTARTED AT ZZ.Z° TO
CONTINUE PRESS ENTER

7
If selftest fails you will get appropriate message
from the list below.
PLEASE RESTART CYCLER Reaction module has exceeded maximum
PLEASE CALL BIO-RAD FOR temperature of 107.5°C or sensor has a

8
SERVICE BLOCK malfunction and is not measuring
OVERHEATED
PLEASE RESTART CYCLER Heatsink temperature has exceeded 60°C. Protocol
HEATSINK OVERHEATED terminated.
PLEASE CALL BIO-RAD FOR
SERVICE
PLEASE RESTART CYCLER Amplifier 1 temperature has exceeded 60°C.
9 10 11
SYSTEM OVERHEATED Protocol terminated.
PLEASE
CALL BIO-RAD FOR SER-
VICE
PLEASE CALL BIO-RAD FOR All block sensors have failed (see below for failure
SERVICE criteria). Protocol terminated.
ALL BLOCK SENSORS
FAILED

10013582B 11/08 8-7


Troubleshooting

Error Message Description


PLEASE CALL BIO-RAD FOR Power Supply temperature has exceeded 70°C.
SERVICE Protocol terminated.
POWER SUPPLY OVER-
HEATED
PLEASE CALL BIO-RAD FOR Lid sensor has failed during lid preheat. Protocol
SERVICE terminated.
HEATED LID FAILED
PROTOCOL CANCELLED
PLEASE CHECK AIRFLOW Heatsink has exceeded 50°C. System beeps and
HTSINK OVERHEATING displays error.
PLEASE CALL BIO-RAD FOR
SERVICE
PLEASE CHECK AIRFLOW Amp temp has exceeded 50°C. System beeps and
SYSTEM OVERHEATING displays error.
PLEASE CALL BIO-RAD FOR
SERVICE
PLEASE CHECK AIRFLOW Power Supply temperature has exceeded 55°C.
PS OVERHEATING PLEASE System beeps and displays error.
CALL BIO-RAD FOR SER-
VICE
PLEASE CALL BIO-RAD Block failed to achieve target in the estimated
FOR SERVICE time.
SLOW BLOCK CYCLING
PLEASE CALL BIO-RAD Lid failed to achieve target in the estimated time.
FOR SERVICE
SLOW LID CYCLING
PLEASE CALL BIO-RAD Block failed to achieve gradient in the estimated
FOR SERVICE time.
SLOW GRADIENT
PLEASE CALL BIO-RAD (singles only) If the right and left lid heater
FOR SERVICE channels deviate from each other by more than
HEATED LID FAILED 5°C, the protocol is terminated and the block sent
to 4C to preserve samples
PLEASE CALL BIO-RAD Block sensor 0 has failed* and the protocol was
FOR SERVICE terminated.
BLOCK SENSOR 0
FAILED
PLEASE CALL BIO-RAD Block sensor 1 has failed* and the protocol was
FOR SERVICE terminated.
BLOCK SENSOR 1
FAILED
PLEASE CALL BIO-RAD Block sensor 2 has failed* and the protocol was
FOR SERVICE terminated.
BLOCK SENSOR 2
FAILED

8-8 10013582B 11/08


Troubleshooting

Error Message Description


PLEASE CALL BIO-RAD Block sensor 3 has failed* and the protocol was

1
FOR SERVICE terminated.
BLOCK SENSOR 3
FAILED
PLEASE CALL BIO-RAD Block sensor 4 has failed* and the protocol was
FOR SERVICE terminated.

2
BLOCK SENSOR 4
FAILED
PLEASE CALL BIO-RAD Block sensor 5 has failed* and the protocol was
FOR SERVICE terminated.

3
BLOCK SENSOR 5
FAILED
PLEASE CALL BIO-RAD Left lid sensor has failed*. If a dual, protocol
FOR SERVICE terminated. If a single and BOTH lid sensors

4
LEFT LID SENSOR failed, protocol terminated and block sent to 4°C.
FAILED
PLEASE CALL BIO-RAD Right lid sensor has failed*. If a dual, protocol
FOR SERVICE terminated. If a single and BOTH lid sensors
RIGHT LID SENSOR failed, protocol terminated and block sent to 4°C.

5
FAILED
PLEASE CALL BIO-RAD Left heatsink sensor has failed*, system using
FOR SERVICE average of amplifier temperatures to continue.
LEFT HEATSINK SENSOR

6
FAILED
PLEASE CALL BIO-RAD Right heatsink sensor has failed* system using
FOR SERVICE average of amplifier temperatures to continue.
RIGHT HEATSINK SENSOR
FAILED

7
PLEASE CALL BIO-RAD (duals only) Lid has overheated and has been
FOR SERVICE shut off and protocol has been terminated.
LID OVERHEATED AND
WAS SHUT OFF

8
PLEASE CALL BIO-RAD Amplifier temperature sensor 1 has failed
FOR SERVICE
AMP1 TEMP SENSOR
FAILED
PLEASE CALL BIO-RAD
FOR SERVICE
POWER SUPPLY SENSOR
Power Supply sensor has failed
9 10 11
FAILED
PLEASE CALL BIO-RAD Power to block is out of range.
FOR SERVICE
BLOCK POWER FAILURE
PROTOCOL CANCELLED
PLEASE CALL BIO-RAD Logic power sensor is out of bounds.
FOR SERVICE LOGIC
POWER FAILURE

10013582B 11/08 8-9


Troubleshooting

Error Message Description


PLEASE CALL BIO-RAD Base power sensor is out of bounds. Protocol
FOR SERVICE cancelled.
BASE POWER FAILURE
PROTOCOL CANCELLED
PLEASE CALL BIO-RAD Amplifier temperature sensor 2 has failed
FOR SERVICE
AMP2 TEMP SENSOR
FAILED
BLOCK MISSING Reaction module has been removed. Protocol
PROTOCOL CANCELLED terminated.
PLEASE CALL BIO-RAD
FOR SERVICE
PLEASE CALL BIO-RAD Protocol storage memory has been corrupted.
FOR SERVICE MEMORY
CORRUPT PROTOCOLS
MAY BE LOST
PLEASE RESTART CYCLER Unable to read information from reaction module
BAD REACTION MODULE properly.
PLEASE CALL BIO-RAD
FOR SERVICE
PLEASE RESTART CYCLER Information read from reaction module appears
INCORRECT CHECKSUM incorrect.
PLEASE CALL BIO-RAD
FOR SERVICE
PLEASE RESTART CYCLER There was a problem with the block and power
BLOCK POWER SHUT OFF was shut off
PLEASE CALL BIO-RAD
FOR SERVICE

8-10 10013582B 11/08


Troubleshooting

8.2.3 Troubleshooting Guide

1
Problem Cause Solution
Noisy run X-slide • No biase down on X rail end on • Remove belt tension, remove
rail. U-shape X-rail support,
remount X rails for 3mm biase

2
• Shuttle hitting obstruction.
and re-tension belt, reinstall X-
• Dry X-rail. rail support.
• Wrong belt tension.
• Re-install shuttle-mount against

3
sliding block; check cleanli-
ness under shuttle in motion
path.
• apply few drops of lubricant oil
to sliding block.

4
• Check belt tension ( for 5.5 lb ),
remove lock 2set screws,
adjust tension and install lock
set-screws

5
Noisy run Y-slide • Dry Y-rail. • apply few drops of lubricant oil
to sliding block.
• Wrong belt tension.
• Check belt tension ( for 6.5 lb ),
remove lock 2set screws,

6
adjust tension and install lock
set-screws
Bad Scan data/inaccuracy X-slide • Set screw at pulley is loose. • Retighten or replace pulley.
• Wrong belt tension. • Check belt tension ( for 5.5 lb ),

7
remove lock 2set screws,
• Xstart position wrong.
adjust tension and install lock
• X-slide not parallel with Rows. set-screws.
• Shuttle hitting obstruction. • Alignment with Laser fixture or

8
Pin gauge.
• Alignment with gauge.
• Re-install shuttle mounting
against sliding block; check
cleanliness under shuttle in
motion path. 9 10 11
Bad Scan data/inaccuracy Y-slide • Shuttle hitting obstruction. • Retighten or replace pulley.
• Set screw at pulley is loose. • Check belt tension ( for 6.5 lb ),
remove lock 2set screws,
• Wrong belt tension.
adjust tension and install lock
• Y start position wrong. set-screws.
• Alignment with Laser fixture or
Pin gauge.
Bad Scan data/inaccuracy Flex-cable/ • Broken shuttle flex-cable • Replace shuttle flex-cable
upper board assembly

10013582B 11/08 8-11


Troubleshooting

Problem Cause Solution


Bad Scan data/inaccuracy Shuttle • Broken shuttle. • Replace shuttle
Bad Scan data/inaccuracy Heater Block • Mis-aligned heater plate. • Re-align heater plate.
Assembly
• Broken thermal fuse or thermis- • Replace thermal fuse or therm-
tor. istor.
Bad Scan data/inaccuracy Main PCB • Broken PCB. Corrupted ROM • Replace PCB. Re-load ROM.
data.
Bad Scan data/inaccuracy XY stage • Dirty reference spots • Clean reference spots
assembly
Bad Scan data/inaccuracy Frame • Broken cooling fans • Replace cooling fans
Assembly
Fail start up self-test X-slide • Shuttle not reaching limit • Remove belt tension, re-install
switch. shuttle-mount and re-tension
belt.
• Broken optical home sensor.
• Replace sensor.
• Broken stepper /connector.
• Replace stepper/ connector.
• Set screw at pulley is loose
• Retighten or replace pulley.
Fail start up self-test Y-slide • Shuttle not reaching limit • Remove belt tension, re-install
switch. shuttle-mount and re-tension
belt.
• Broken optical home sensor.
• Replace sensor.
• Broken stepper /connector.
• Replace stepper/ connector.
• Set screw at pulley is loose
• Retighten or replace pulley.
Fail start up self-test Shuttle • Broken shuttle • Replace shuttle
Fail start up self-test Frame Assembly • Loose Main Power Harness • Reconnect Main Power Har-
10007589. ness 10007589, both ends
• Mis-adjusted Lid positioner • Re-adjusted Lid positioner
switch. switch
• Broken Lid positioning motor/ • Replace Lid positioning motor/
connector connector
Fail start up self-test Heater Block • Damage heater element. • Replace heater assembly or
Assembly element
• Broken thermal fuse or thermis-
tor • Replace thermal fuse or therm-
istor.
• Loose power connection to
main board • Loose power connection to
main board.
Fail start up self-test Hinge motor • Broken torsion spring. • Replace torsion spring.
• Loose set screw at motor shaft. • Retighten screw.
• Broken hinge motor/ connector. • Replace hinge motor/ connector
Fail start up self-test Main PCB • Damage PCB. • Replace PCB.
• Corrupted ROM data • Re-load ROM

8-12 10013582B 11/08


Troubleshooting

Problem Cause Solution


Fail start up self-test Front Motor • Set screw at front motor is • Retighten or replace screw and

1
Assembly loose. motor.
• Broken motor /connector. • Replace motor/ connector.
• Broken motor sensor. • Replace sensor.

2
• Broken spur gears • Replace spur gears
Fail start up self-test Cables layout • Cable wiring interfere with slide • Route cable, wiring to clear
motions slide motions
Sample loss during PCR Frame Assem- • Mis-adjusted Lid positioner • Re-adjusted Lid positioner
bly switch. switch.

3
• Mis-alignment Alpha Block. • Re-align Alpha Block
Sample loss during PCR Main PCB • Corrupted ROM data • Re-load ROM
Sample loss during PCR Lid plate sen- • Broken plate/tube detection • Replace heater assembly or

4
sor sensor. repair sensor/solder joint.
• Mis-aligned front flag • Re-aligned front flag
Cannot open Lid with switch Frame • Loose Main Power Harness • Re-connect Main Power Har-
Assembly 10007589. ness 10007589, both ends.

5
• Broken Front switch/connector • Replace Front switch/connec-
tor.
Cannot open Lid with switch Hinge • Broken torsion spring. • Replace torsion spring.
motor
• Loose set screw at motor shaft. • Re-tighten screw.

6
• Broken hinge motor/ connector. • Replace hinge motor/ connector
Cannot open Lid with switch Front • Set screw at front motor is • Re-tighten or replace screw and
Motor Assembly loose. motor.

7
• Broken motor /connector. • Replace motor/ connector.
• Broken motor sensor. • Replace sensor.
• Broken spur gears. • Replace spur gears .

8
9 10 11

10013582B 11/08 8-13


Parts

Section 9
Parts

1
9.1 Introduction

2
This section contains parts lists and associated information. It provides instructions for ordering and returning
defective parts. This section also identifies parts that are field irreplaceable.

3
9.2 Parts Orders - US Domestic Operations
Parts may be ordered through our Service Parts department. You can reach the Service Parts department
during Pacific time regular office hours by calling 1-510-741-5038, 5058, 5071 or 5263. You can help to make
processing your order more efficiently by having the following information before you call:

4
• The part number(s) or catalog number(s) of the parts you want to order
• Shipment information
• Your account or inventory location number

5
9.3 Parts Orders - International Subsidiaries
The procedures for ordering parts vary from region to region outside the United States. Please contact your
Bio-Rad Export Sales Representative through your regular sales and service channels.

6
9.4 Returning Defective Parts

7
Mail-in products do not contain returnable parts or assemblies.

9.5 Recommended Spares

8
The appropriate quantity for each of the CFX96/CFX384 Real-Time System spares will vary depending on the
total quantity of instruments in your installed base. A quantity of 1 for each field irreplaceable part is a good
starting point.

9 10 11

10013582B 11/08 9-1


Parts

Recommended Spares List

Part Number Description Picture


10012843 CFX96/CFX384 PCB Main
Board

10013072 CFX96/CFX384 FCC w/INT


PCB Assy

10013073 CFX96 Minco Heater

10013085 CFX96 Heater Cover Plate

10013066 CFX96 Stage Carrier

10013076 CFX96/CFX384 Hinge Motor


Assy

9-2 10013582B 11/08


Parts

Recommended Spares List

1
Part Number Description Picture
10013080 CFX96/CFX384 Hinge Assy

2
10013081 CFX96/CFX384 Front Motor

3
Assy

4
10013082 CFX96/CFX384 Pinion, Front

5
Motor

6
10013083 CFX96/CFX384 Lid Position
Gear Box

7
8
10013077 CFX96/CFX384 Fan Assy.
Qty(2)

9 10 11
10013068 CFX96/CFX384 Micro Switch

10013582B 11/08 9-3


Parts

Recommended Spares List

Part Number Description Picture


10013069 CFX96/CFX384 XY Axis Sen-
sor

10013078 CFX96/CFX384 Hinge Lim


Sens Harness

10013079 CFX96/CFX384 Front Lim Sens


Harness

10013070 CFX96/CFX384 Reference


Spots

10013084 CFX96/CFX384 Pod Switch


Assy

9-4 10013582B 11/08


Parts

Recommended Spares List

1
Part Number Description Picture
10013441 CFX96 Real-Time Alpha Block

2
3
4
10013442 CFX96 Alpha O-Ring

5
10013074 CFX96 Case Assy

6
7
10013075 CFX96 Shipping Screw

8
9 10 11

10013582B 11/08 9-5


Parts

Recommended Spares List

Part Number Description Picture


10015187 CFX96/CFX384 Base Plate
Overlay

10015188 CFX384 Real Time Alpha

10015190 CFX384 Lid heater Assembly.


Includes Heater Plate.

10015191 CFX384 Housing Assembly

9-6 10013582B 11/08


Parts

Recommended Spares List

1
Part Number Description Picture
10015192 CFX384 Stage Carrier Assembly

2
3
10015186 CFX384 Shipping Screw

4
10015194 CFX96/CFX384 Main Board
Battery

5
6
10015195 C1000 Main Board Fuses:

5A 250V Fast 5x20mm Qty 1


0.5A 250VSLO 5x20mm Qty 1

7
Blade Mini 20A 32V Qty3
Blade Mini 2A 32V Qty 1

8
10013443 Tool, CFX Motor & Sensor Test
Box

9 10 11
10013444 Tool, CFX96 Ultem Plate

10013582B 11/08 9-7


Parts

Recommended Spares List

Part Number Description Picture


10015198 Tool, CFX384 Ultem Plate

Tool, CFX384 Heater plate


Alignment Pins

10013445 Tool, CFX96 Heater Plate Align-


ment Pins. Qty(8)

Tool, Hinge Alignment Fixture

10013446 Tool, CFX Shuttle Pin Check

10015189 Snap Rivets. Qty(7)

9-8 10013582B 11/08


Parts

Recommended Spares List

1
Part Number Description Picture
10010780 C1000/S1000 Main Board

2
3
10014633 C1000 Fuse 10A, 250V,
5X20mm. Qty 2

4
10010781 C1000 Controller PCB

5
6
10010788 C1000 Controller Battery Pack

7
8
10010779 C1000 Alpha interconnect PCB

9 10 11
10010782 C1000 USB Connector PCB

10013582B 11/08 9-9


Parts

Recommended Spares List

Part Number Description Picture


10010784 C1000 USB Thumb key PCB

10010759 C1000 Power Entry

10010756 C1000 Fan Assy

10010770 C1000 AI Sensor Cable

10010771 C1000 TE Power Cable

10010772 C1000 Lid Power Cable

9-10 10013582B 11/08


Parts

Recommended Spares List

1
Part Number Description Picture
10010773 C1000 USB to Main Cable

2
3
10010776 C1000 ON/Off Switch

4
10010777 C1000 USB Jumper Cable

5
6
10010785 C1000 Braided EMI Cable

7
10010768 C1000 Keypad

10010767 C1000 Latch .L.R


8
9 10 11

10013582B 11/08 9-11


Parts

Recommended Spares List

Part Number Description Picture


10010789 C1000 Latch Springs

10010760 C1000 Case Bottom

10010761 C1000 Case Top

10010762 C1000 Case Side Bands .L.R

10010763 C1000 Front Vents.L.R

10010764 C1000 Feet

9-12 10013582B 11/08


Parts

Recommended Spares List

1
Part Number Description Picture
10010766 C1000 Latch handle

2
3
10013148 1000 Alpha Test Fixture

4
5
6
7
8
9 10 11

10013582B 11/08 9-13


Drawings

Section 10
Drawings

1
10.1 About this Section

2
This section contains schematics and assembly drawings for the CFX96 Real Time System. These drawings are intended
to be used as aids for troubleshooting and parts identification.

10.2 Drawings

3
• Main Board 2 page
• Detector Board 1 page

4
• Led ADC Board 1 page
• Open/Close PCB 1 page
• Shuttle Transition Board 1 page

5
• Upper Board 1 page
• X-Axis Board 1 page

10.3 Schematics

6
• CFX96 Main PCB Schematic 3 pages
• Lid Heater Schematic 1 page

7
• X-Axis Board Schematic 1 page
• Upper Board CFX96 Schematic 3 page
• LED ADC CFX96 1 page

8
• Shuttle Transition CFX96 1 page
• Open/Closed CFX96 1 page

9 10 11

10013582B 11/08 10-1


SCHEM,PCB,X-AXIS,SIERRA.sch-1 - Tue Oct 02 11:06:32 2007
SchemDWG,OPEN_CLOSED,SIERRA.sch-1 - Tue Oct 02 10:52:43 2007
INT.
Appendix

Section 11
Appendix

1
Appendix A

2
11.1 CFX96/ CFX384 Installation Report
This section is the Installation Report for the CFX96/CFX384 Real Time System as performed in the Installa-
tion section with additional recording of information on the report. Successful completion of the Installation sec-

3
tion represents the verification of instrument installation. This report should be filed for record keeping.

4
5
6
7
8
9 10 11

10013582B 11/08 11-1


Appendix

CFX96 Real Time System


Installation Report

Customer: Instrument Model


Case Number: Instument Serial Number

Test Specification Results


Visual Inspection
No signs of damage ‰ Pass ‰ Fail
All contents and accessories received: ‰ Pass ‰ Fail
C1000 Chassis ‰ Pass ‰ Fail
CFX96 ‰ Pass ‰ Fail
Power Cord ‰ Pass ‰ Fail
Fuses ‰ Pass ‰ Fail
Operating Manual ‰ Pass ‰ Fail
Warranty Card ‰ Pass ‰ Fail
CFX Manager Software ‰ Pass ‰ Fail

Power Line Requirements Line Voltage Check: Record AC line voltage_______________ ‰ Pass ‰ Fail

Serial Number Instrument Serial Number:


CFX96 S/N________________________ ‰ Pass ‰ Fail

C1000 Chassis S/N________________________ ‰ Pass ‰ Fail

Alpha Reaction Block S/N________________________ ‰ Pass ‰ Fail

Instrument Firmware Firmware Version:

C1000 Chassis HC12 Firmware Ver. ____________ ‰ Pass ‰ Fail


C1000 Chassis PAX270 Firmware Ver. ____________ ‰ Pass ‰ Fail
C1000 Chassis FX2 Firmware Ver. ____________ ‰ Pass ‰ Fail
CFX96 Optical Module 8051 Firmware Ver. ____________ ‰ Pass ‰ Fail
CFX96 Optical Module DSP Firmware Ver. ____________ ‰ Pass ‰ Fail

Start Up Power-up self-test ‰ Pass ‰ Fail


Display Check ‰ Pass ‰ Fail
Fan Check ‰ Pass ‰ Fail
CFX Manager Installed on PC ‰ Pass ‰ Fail
CFX Manager communicates with CFX96 ‰ Pass ‰ Fail

Diagnostic test C1000 Chassis Diagnostic test ‰ Pass ‰ Fail

11-2 10013582B 11/08


Appendix

1
The above referenced instrument has been installed and meets all Installation requirements.

2
Comments:

3
Bio–Rad Labs Service Date

4
5
6
7
8
9 10 11

10013582B 11/08 11-3


Appendix

CFX384 Real Time System


Installation Report

Customer: Instrument Model


Case Number: Instument Serial Number

Test Specification Results


Visual Inspection
No signs of damage ‰ Pass ‰ Fail
All contents and accessories received: ‰ Pass ‰ Fail
C1000 Chassis ‰ Pass ‰ Fail
CFX384 ‰ Pass ‰ Fail
Power Cord ‰ Pass ‰ Fail
Fuses ‰ Pass ‰ Fail
Operating Manual ‰ Pass ‰ Fail
Warranty Card ‰ Pass ‰ Fail
CFX Manager Software ‰ Pass ‰ Fail

Power Line Requirements Line Voltage Check: Record AC line voltage_______________ ‰ Pass ‰ Fail

Serial Number Instrument Serial Number:


CFX384 S/N________________________ ‰ Pass ‰ Fail

C1000 Chassis S/N________________________ ‰ Pass ‰ Fail

Alpha Reaction Block S/N________________________ ‰ Pass ‰ Fail

Instrument Firmware Firmware Version:

C1000 Chassis HC12 Firmware Ver. ____________ ‰ Pass ‰ Fail


C1000 Chassis PAX270 Firmware Ver. ____________ ‰ Pass ‰ Fail
C1000 Chassis FX2 Firmware Ver. ____________ ‰ Pass ‰ Fail
CFX96 Optical Module 8051 Firmware Ver. ____________ ‰ Pass ‰ Fail
CFX96 Optical Module DSP Firmware Ver. ____________ ‰ Pass ‰ Fail

Start Up Power-up self-test ‰ Pass ‰ Fail


Display Check ‰ Pass ‰ Fail
Fan Check ‰ Pass ‰ Fail
CFX Manager Installed on PC ‰ Pass ‰ Fail
CFX Manager communicates with CFX96 ‰ Pass ‰ Fail

11-4 10013582B 11/08


Appendix

Diagnostic test C1000 Chassis Diagnostic test ‰ Pass ‰ Fail

1
2
The above referenced instrument has been installed and meets all Installation requirements.

Comments:

3
4
Bio–Rad Labs Service Date

5
6
7
8
9 10 11

10013582B 11/08 11-5


Appendix

11.2 CFX96/CFX384 Operational Report


This section is the Operational Report of the CFX96/CFX384 Real Time Systems as performed in the System
Checkout section. Successful completion of the tests in the System Checkout section represents a complete
functional check of all system components.

11-6 10013582B 11/08


Appendix

1
CFX96 Real Time System
Operational Report

2
Customer Instrument Serial Number:

Case Number: AC Input Voltage: ‰ 100v ‰ 120v ‰ 220v ‰ 240v

3
Test Specification Results

Instrument Condition Alpha Block Cleanliness ‰ Pass ‰ Fail


LCD Display Function ‰ Pass ‰ Fail

4
Power-on Self-Test ‰ Pass ‰ Fail
CFX Manager Communication ‰ Pass ‰ Fail
________
C1000 Diagnostic Test C1000 Diagnostic Test ‰ Pass ‰ Fail

5
First Attached S1000 Diagnostic Test ‰ N/A ‰ Pass ‰ Fail
Second Attached S1000 Diagnostic Test ‰ N/A ‰ Pass ‰ Fail
Third Attached S1000 Diagnostic Test ‰ N/A ‰ Pass ‰ Fail

6
USB Thumb key Transfer Diagnostic test Result to PC using USB thumbkey ‰ Pass ‰ Fail

7
8
9 10 11

10013582B 11/08 11-7


Appendix

CFX System Test CFX System Test Result: ‰ Pass ‰ Fail

Query Firmware Version ‰ Pass ‰ Fail


Query Serial Number ‰ Pass ‰ Fail
Optical Head Self Test ‰ Pass ‰ Fail
Verify Block Indicator ‰ Pass ‰ Fail
Verify Lid Open/Close using case push button ‰ Pass ‰ Fail
Detect Lid Obstruction ‰ Pass ‰ Fail
Test Lid in Auto Mode - Low Plate ‰ Pass ‰ Fail
Test Lid in Manual Mode - Low Plate ‰ Pass ‰ Fail
Test Lid in Auto Mode - Low Tube ‰ Pass ‰ Fail
Test Lid in Auto Mode - High Plate ‰ Pass ‰ Fail
Test Lid in Manual Mode - High Plate ‰ Pass ‰ Fail
Test Lid Obstruction in Manual Mode - High Plate ‰ Pass ‰ Fail
Test Lid in Auto Mode - High Tube ‰ Pass ‰ Fail
Base Unit Fan ‰ Pass ‰ Fail
Case Fan ‰ Pass ‰ Fail
Check Pin ‰ Pass ‰ Fail
Rotated Plate Uniformity Check ‰ Pass ‰ Fail
Reference Row check (no plate required) ‰ Pass ‰ Fail
Bare Block Scan for contamination ‰ Pass ‰ Fail
Base Unit Self Test ‰ Pass ‰ Fail
Optical Head Check ‰ Pass ‰ Fail
Shuttle Slots Valid ‰ Pass ‰ Fail
Shuttle Slots Calibrated ‰ Pass ‰ Fail
Verify Lid Open/Close Using Motorized Command ‰ Pass ‰ Fail
Verify Block Performance ‰ Pass ‰ Fail
Verify Lid Heating ‰ Pass ‰ Fail
Verify Shuttle EEPROM ‰ Pass ‰ Fail
System EEPROM ‰ Pass ‰ Fail
Thermal Validation Test Validation Result Printout Attachment ‰ Not Applicable
‰ Yes ‰ No ‰ N/A
C1000 Certificate Printout Completed ‰ Not Applicable
‰ Yes ‰ No ‰ N/A
Thermal Validation Contract ‰ Not Applicable
‰ Yes ‰ No ‰ N/A

Specification: ‰ Pass ‰ Fail


Accuracy ___________________ ‰ Pass ‰ Fail
Uniformity ___________________ ‰ Pass ‰ Fail

11-8 10013582B 11/08


Appendix

Lid Heater Test


(OPTIONAL) Record Lid Temperature ________°C

1
‰ Pass ‰ Fail

Test Equipment Standards

2
Calibration Model Description Serial Number Cal Date Cal Due
Date
Control Number

3
The above referenced instrument meets all performance specifications requirements.

4
Comments:

Bio-Rad Labs Service Date

5
6
7
8
9 10 11

10013582B 11/08 11-9


Appendix

CFX384 Real Time System


Operational Report

Customer Instrument Serial Number:

Case Number: AC Input Voltage: ‰ 100v ‰ 120v ‰ 220v ‰ 240v

Test Specification Results

Instrument Condition Alpha Block Cleanliness ‰ Pass ‰ Fail


LCD Display Function ‰ Pass ‰ Fail
Power-on Self-Test ‰ Pass ‰ Fail
CFX Manager Communication ‰ Pass ‰ Fail
________
C1000 Diagnostic Test C1000 Diagnostic Test ‰ Pass ‰ Fail

First Attached S1000 Diagnostic Test ‰ N/A ‰ Pass ‰ Fail


Second Attached S1000 Diagnostic Test ‰ N/A ‰ Pass ‰ Fail
Third Attached S1000 Diagnostic Test ‰ N/A ‰ Pass ‰ Fail

USB Thumb key Transfer Diagnostic test Result to PC using USB thumbkey ‰ Pass ‰ Fail

11-10 10013582B 11/08


Appendix

CFX System Test CFX System Test Result: ‰ Pass ‰ Fail

1
Query Firmware Version ‰ Pass ‰ Fail
Query Serial Number ‰ Pass ‰ Fail
Optical Head Self Test ‰ Pass ‰ Fail
Verify Block Indicator ‰ Pass ‰ Fail
Verify Lid Open/Close using case push button ‰ Pass ‰ Fail

2
Detect Lid Obstruction ‰ Pass ‰ Fail
Base Unit Fan ‰ Pass ‰ Fail
Case Fan ‰ Pass ‰ Fail
Check Pin ‰ Pass ‰ Fail

3
Rotated Plate Uniformity Check ‰ Pass ‰ Fail
Reference Row check (no plate required) ‰ Pass ‰ Fail
Bare Block Scan for contamination ‰ Pass ‰ Fail
Base Unit Self Test ‰ Pass ‰ Fail

4
Optical Head Check ‰ Pass ‰ Fail
Shuttle Slots Valid ‰ Pass ‰ Fail
Shuttle Slots Calibrated ‰ Pass ‰ Fail
Verify Lid Open/Close Using Motorized Command ‰ Pass ‰ Fail
Verify Block Performance ‰ Pass ‰ Fail

5
Verify Lid Heating ‰ Pass ‰ Fail
Verify Shuttle EEPROM ‰ Pass ‰ Fail
System EEPROM ‰ Pass ‰ Fail

6
Thermal Validation Test Validation Result Printout Attachment ‰ Not Applicable
‰ Yes ‰ No ‰ N/A
C1000 Certificate Printout Completed ‰ Not Applicable
‰ Yes ‰ No ‰ N/A

7
Thermal Validation Contract ‰ Not Applicable
‰ Yes ‰ No ‰ N/A

8
Specification: ‰ Pass ‰ Fail
Accuracy ___________________ ‰ Pass ‰ Fail
Uniformity ___________________ ‰ Pass ‰ Fail

9 10 11
Lid Heater Test
(OPTIONAL) Record Lid Temperature ________°C

‰ Pass ‰ Fail

Test Equipment Standards

Calibration Model Description Serial Number Cal Date Cal Due


Date
Control Number

10013582B 11/08 11-11


Appendix

The above referenced instrument meets all performance specifications requirements.

Comments:

Bio-Rad Labs Service Date

11-12 10013582B 11/08

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