Software Verification Report



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Software Release Memo

|PRODUCT FAMILY: |IsoCyte |

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|PROJECT: |5.1.3 |

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|AUTHOR: |Evan Cromwell |

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|PROJECT MANAGER: |Mike Youngquist |

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|ELECTRONICALLY CONTROLLED DOCUMENT |

|ONCE PRINTED, VERIFY REVISION PRIOR TO USE |

|DO NOT MARK OR ALTER |

|RELEASE APPROVAL: | |REVIEWED/APPROVED BY: |

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|NAME: |KEITH PRICE |Bryan Gittens |

|TITLE: |SENIOR VP, QUALITY & REGULATORY AFFAIRS |Software Verification DPO |

[Document] Revision History

|Revision |Date |Author |Description of Change |

|A |2011-01-13 |Evan Cromwell |Initial Release |

|B |2011-02-13 |Evan Cromwell |Update doc for 5.1.3 |

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| | | | |

TABLE OF CONTENTS

1.0 SUMMARY 4

1.1 Project Overview 4

1.2 Verification Testing 4

2.0 REFERENCES 4

3.0 DEFINITIONS 4

4.0 SW & FW REVISIONS 5

4.1 Improved Data Acquisition and Analysis 5

4.2 Improved Calibration and Instrument Setup 5

4.3 More Intuitive Messages and Stage Controls 6

4.4 Use of Single Image Viewer 7

4.5 Use of Memory for Data Averaging 8

4.6 Method for Plate Tilt Correction 8

4.7 Scan Abort Button 8

4.8 Other Improvements 8

5 Software Release Information 9

LIST OF FIGURES

Figure 1. Screen shot of successful calibration message 5

Figure 2. Screen shot of failed calibration message 6

Figure 3. Revised Calibration user interface 7

Figure 4. Main IsoCyte user interface sreen 7

Figure 5. Revised Analysis tab in Instrument Setup panel 8

1.0 SUMMARY

1.1 Project Overview

The IsoCyte 5.1.3 project addressed limitations in system performance caused by memory usage schemes and software bugs. The project also included several enhancements to the user interface and implementation of new controls. In this release, both software and firmware updates are provided. The software is version 5.1.3; the firmware is version 1037. They are installed automatically with the IsoCyte installer program. The main features incorporated in the release and the code (SW or FW) in which they reside are:

1. Improved robustness of data acquisition and analysis (SW, FW)

2. Improved robustness of calibration routines (SW)

3. More intuitive system messages and controls for the user (SW)

4. Implementation of stage homing controls (SW)

5. Use of single image viewer (SW)

6. More efficient memory usage for data averaging (SW, FW)

7. Improved method for plate tilt correction (SW, FW)

8. Fix of the Scan Abort function (SW)

In addition, 5.1.3 addressed two issues found with the IsoCyte software version 5.1.2. These are:

1. Inability to open data files in off-line mode (SW)

2. Improper calibration when using Legacy Plastic plate (SW)

Verification Testing

The software was tested and validated according to internal quality procedures. Details of the testing are contained in the Software Verification Report on IsoCyte 5.1.3.

2.0 REFERENCES

None

3.0 DEFINITIONS

SW = Software

FW = Firmware

CPU = Computer Processing Unit

GBE = Gigabit Ethernet

LUT = Look Up Table

ILUT = Intensity Look Up Table

SW & FW REVISIONS

The following changes are implemented in this SW and FW release:

1 Improved Data Acquisition and Analysis

The new IsoCyte SW and FW now allows the users to scan from 6 well to 3456 well plates, up to 4 channels, at any supported sampling without a system crash or hang-up. The data acquisition and analysis of the IsoCyte system is limited by the available memory of the Windows XP operating system and the capabilities of the CPU’s. In the previous version of SW, the system would allocate memory for all selected wells and simultaneously run acquisition and analysis threads through the CPUs. This provided the fastest speed, but would crash when the memory and multi-threading requirements strained the computer, for example, when reading 4 channels of data from 1536 well plates. It was also found that the video display, which also competes for CPU time, could interfere with system stability during demanding operation. Several changes to the architecture were made to overcome these limitations.

1) Scans are setup on a column-by-column basis

2) Data analysis is not begun until after all data has been transferred over the GBE communication line

3) The video display routines were made more efficient and scheduled not to interfere with other operations.

4) Ability to sample at higher resolutions than 2.5 microns has been eliminated

The total scan and analysis time during low data loads (e.g. when using 10 micron sampling and one or two channels) is not significantly affected because analysis occurs between columns. For higher data loads (e.g., 5 micron and/or 3 or 4 channels of data, with Analysis) the total scan time is longer. However, the system does not need to do partial column scans so under very demanding conditions (e.g., 4 channels at 2.5 micron sampling) the total scan time is improved. Re-analysis is distributed among all CPUs and no longer has memory restrictions.

2 Improved Calibration and Instrument Setup

The LUT and ILUT calibration routines for the IsoCyte are critical to obtaining peak performance, but the system messages for Acceptance or Rejection were not clear. New messages, shown below, are provided when calibration is successful and not successful. Users are given a choice of whether to Accept or Cancel calibration. Details of the calibration can be revealed if required, for example, by technical support.

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Figure 1. Screen shot of successful calibration message

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Figure 2. Screen shot of failed calibration message

3 More Intuitive Messages and Stage Controls

The controls in the Instrument Setup panel have been revised so that they are more intuitive and provide proper feedback as to plate movement and location. An image of the updated interface is shown below. Improvements include:

1) The various “Set” buttons are grayed out until a new value has been entered into a box and then they become active.

2) The “Adjust View” command now adjusts the line scan window correctly in units of microns

3) The stage position readouts are now presented as the Position (absolute), Delta (relative to Home position of the Method), and Step Size in microns that one moves the stages up and down or left/right. The Absolute position is stored in the Method as its Home and so is the most important to the user. One can update the Home position of the Method by clicking the “Update Method Home” button

4) The “Use Legacy Plastic Plate” check box is for those users who do not possess an IsoCyte Alignment Plate

5) The “Apply” button function has been changed to update either LUT or ILUT calibration values and then re-start the scan so the User can view the new settings. An “Apply n Quit” button has been added which applies the LUT and/or ILUT calibration and then exits the Calibration screen. (Note: This has the previous functionality of the “Apply” button, but is more descriptive.)

In addition to the above updates, Home buttons have been added for each of the three stages. These allow the user to re-home the stages without having to power cycle the IsoCyte instrument. This can be advantageous if for any reason the stages lose track of Home, or if the user suspect that the stage absolute position measurement has been compromised. It should be noted that the stage Home buttons on the right hand side of the Calibration screen affect the individual stage home positions. The Update Method Home affects the Method home positions which are calculated relative to the stage home positions.

When switching between a “Legacy Plastic Plate” and an “IsoCyte Alignment Plate” the user must update the “Edge to First Rule” and “Rule Spacing” entries with the values provided by the plate to be used for calibration.

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Figure 3. Revised Calibration user interface

4 Use of Single Image Viewer

The Plate Scan mode and the older style viewer that was used in that mode have been removed. Now all images are viewed in the Analysis Mode viewer. This is a much more intuitive and useful viewer. The Display Results tab is still activated by right-clicking on a well. A heat map of those results is then provided to the user. An image of the new interface is shown below.

In addition to this modification, the Export Data tab in the Data menu and the “Save .bbx Files” function in the Instrument Setup panels have been removed. The .bbx file format was used with the older BlueImage programs and is not supported in version 5.1.3. An image of the new Analysis tab in the Instrument Setup panels is shown below.

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Figure 4. Main IsoCyte user interface sreen

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Figure 5. Revised Analysis tab in Instrument Setup panel

5 Use of Memory for Data Averaging

The SW and FW have been updated to more efficiently use memory during data averaging. There has been no change to the data averaging algorithm, but the number of lines of data stored in memory has been reduced to the minimum required amount. This eliminates memory constrictions when using a high number of averages.

6 Method for Plate Tilt Correction

Non-parallel movement of the plate with respect to the laser trigger can cause a shift of the image up or down in a column (Y-direction). This offset is called Plate Tilt. In the previous version a buffer zone around each row was provided for tilt correction and correction was done in FW on a row-by-row basis. However, when Plate Tilt exceeded this buffer size there could be anomalous shifts in the row positions, especially with 1536 well plates. In the new FW the buffer zone has been removed and tilt is adjusted on a line-by-line basis using a pre-calculated LUT. There is no change to the User or setup procedure and no modifications to how data is collected or processed.

7 Scan Abort Button

The Scan Abort button has now been made functional. The user can now abort a scan after it finishes acquiring data from wells in a column. The Abort function in AutoRun is also now functional. In this case, the user needs to first Abort the Scan and then Abort the AutoRun

8 Other Improvements

A Sequential Analysis capability has been added. When this box is checked in the Analysis tab of Instrument Setup the plate is scanned, data acquired, and then analysis is performed.

Various Error Messages have been revised to be more intuitive and helpful to the user.

An issue with false Scanner Trigger errors occurring during Calibration procedures has been resolved.

An issue with Laser Not Available errors occurring during scan setup has been resolved.

Software Release Information

|Iteration Version |Build Number |Released Date |

|5.1.3 |002 |2011-02-14 |

|FW 1037 |n/a |2011-01-12 |

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