ScanArray Microarray Analysis Software Version 3.1 Release Notes Contents of this file --------------------- 1. System requirements for host computer. 2. Changes in Version 3.1 3. Bug fixes in Version 3.1. 4. Known system problems and work-arounds. System Requirements for Host Computer ------------------------------------- The minimum computer requirements to run ScanArray Microarray Analysis Software Version 3.1 are: 1. 300 MHz Pentium II processor 2. 128 MB RAM for Windows NT/Windows 2000 and ScanArray; 256 MB RAM if concurrently running QuantArray and ScanArray 3. 4 GB hard disk, see below 4. CD-ROM 5. 10MB Ethernet network interface card 6. Display capability of 1024 x 768 x 32K colors; 65K colors if running QuantArray 7. 17" color monitor 8. Microsoft Windows NT 4.0 with Service Pack 4 or higher OR Microsoft Windows 2000 9. Microsoft Internet Explorer 5.0 10. Sufficient virtual memory, see below Supported display resolutions ----------------------------- The system supports the following display resolutions: 1280 x 1024 (Large Fonts) 1280 x 1024 (Small Fonts) 1024 x 768 (Small Fonts) Note: The system does not support 1024 x 768 (large fonts) display resolution. Hard disk requirements ---------------------- The amount of hard disk space required to store your images will depend on the number and size of the image files stored on the disk at any one time. The size of the image files created by ScanArray is dependent on the scanning resolution. The following chart provides estimates for the amount of hard disk space required for a single acquisition and for a set of 50 acquisitions. Please note that an instrument with an autoloader can perform up to 20 acquisitions in a single batch set. #fluors/ scan disk space for disk space for microarray resolution single microarray 50 microarrays ---------- ---------- ----------------- -------------- 1 5 microns 125 MB 6 GB 1 10 microns 30 MB 1.5 GB 2 5 microns 250 MB 12 GB 2 10 microns 60 MB 3 GB 3 5 microns 375 MB 18 GB 3 10 microns 90 MB 4.5 GB 4 5 microns 500 MB 25 GB 4 10 microns 120 MB 6 GB 5 5 microns 625 MB 31 GB 5 10 microns 150 MB 7.5 GB Virtual memory requirements --------------------------- All computer programs require RAM (Random Access Memory) while they are running to store the results of the operations they perform. The amount of RAM required by a computer program varies, depending on the operations it performs and the system configuration. To achieve optimal performance from a computer program, your workstation should have enough RAM to accommodate the operating system requirements plus those of any application programs that are run concurrently. Most operating systems today (Windows NT and 2000 included) can accommodate a smaller amount of RAM by using a technique called "swapping", where the operating system moves data between RAM and the hard disk as it is needed. The technique of using hard disk space to extend the amount of RAM available to a program is called virtual memory. Using virtual memory to compensate for insufficient RAM degrades the performance of the application program and does not remove the requirement for a minimum amount of RAM. It does allow programs to run with a less-than-optimum amount, though. The minimum amount of RAM required to run Windows NT and ScanArray is described earlier in this section. ScanArray uses RAM to save image data during an acquisition and to display the acquired images. The following chart provides estimates for the amount of RAM required by ScanArray, depending on how you use the instrument. The memory requirements assume that you are performing a full-slide scan (22mm x 73mm), displaying images while you scan, and all images are left open during the scan. QuantArray uses RAM to display images and to perform image processing and data analysis. For your convenience, the chart below contains a column describing the memory requirements if you scan images with ScanArray while you analyze previously-scanned images with QuantArray on the same computer. The memory requirements assume that you are performing a full-slide scan, displaying images while you scan, and all images are left open during the scan and analysis. #fluors/ scan ScanArray memory ScanArray+QuantArray microarray resolution requirements memory requirements ---------- ---------- ---------------- -------------------- 1 5 microns 185 MB 887 MB 1 10 microns 45 MB 224 MB 2 5 microns 245 MB 1,385 MB 2 10 microns 60 MB 344 MB 3 5 microns 305 MB 1,755 MB 3 10 microns 75 MB 434 MB 4 5 microns 365 MB 2,125 MB 4 10 microns 90 MB 524 MB 5 5 microns 425 MB 2,495 MB 5 10 microns 105 MB 614 MB To determine the total amount of memory required for the host computer, you should add the amount of RAM specified here to the amount of memory required by Windows NT and other applications you run concurrently on the same computer. To specify the amount of disk space that Windows NT uses for virtual memory, perform the following steps: 1. Open the Windows NT Control Panel by clicking "Start", "Settings", "Control Panel". 2. Double click on the System icon. 3. Select the "Performance" tab. 4. Click the "Change" button to change the "Total Paging File Size for all Volumes". 5. Set the initial page file size to the amount of virtual memory required for the programs you run concurrently, using the recommendations above for running ScanArray by itself. Set the maximum page file size to a value that is 20% greater than the initial page file setting. Changes and New features in Version 3.1 --------------------------------------- 1. Supports Windows 2000. 2. Supports Context sensitive help. 3. Line scan registry fix is now part of Install. 4. ScanArray 3.1, by default, is installed to the folder Packard BioChip if a previous version of ScanArray is not detected on the target system. 5. The Auto-Balance, Auto-Range feature (ABAR) has been improved to provide more accurate results. 6. The option to run ABAR automatically as part of the acquisition protocol has been added by checking the Auto-Range before every scan checkbox. If this checkbox is checked, ABAR will run automatically in both manual and batch mode. 7. Software calibration of instruments to account for mechanical variations along the y-axis of the sample holder was introduced in ScanArray 3.0 and was available to customers with instruction from Packard BioChip service personnel. In ScanArray 3.1, instructions on performing this software calibration are available in the appendix of the User Manual. Bug Fixes in Version 3.1 ------------------------ 1. The client software was unable to open an image file if there is a period in the file path. This did not include the period that separates the image file name and extension. For example, the image file in the path C:\ScanArray3.0\Image.tif could not be opened by the software because there is a period in "ScanArray3.0". ScanArray 3.1 fixes this problem. 2. Selecting Pixel Line tool did not position to the correct protocol in the Line Scan dialog all the time. It always positioned to the protocol used by last acquire. ScanArray 3.1 fixes this problem. 3. ScanArray 3.0 did not save all the Line Scan Parameters properly. ScanArray 3.1 fixes this problem. 4. ScanArray occasionally used to stop responding when Email notification option was selected in Batch Set dialog. ScanArray 3.1 fixes this problem. 5. Very rarely, the instrument software will repeat the same row in a scan for 5 seconds, causing elongated spots. ScanArray 3.1 fixes this problem. 6. Occasionally, when running Auto-Focus or ABAR with multiple fluorophores, the process would appear to be completed and the OK button would be re-enabled while the process continues. ScanArray 3.1 fixes this problem. 7. When running batch sets, a problem occurred when the barcode is used on a microarray and then subsequent microarrays did not use the barcode. An error occurs which states that a barcode could not be found on the microarray that is not using a barcode. ScanArray 3.1 fixes this problem. 8. Occasionally the first install failed and the users had to install ScanArray twice to get it running. This problem is fixed in ScanArray 3.1 setup. Known System Problems and Work-arounds -------------------------------------- 1. Very rarely, the client software will lose the connection to the instrument software during a 5-micron or 10-micron scan. This problem typically occurs when the virtual memory limit is exceeded on the host computer. When this situation occurs, determine the number of images that were remaining to be scanned for the given slide when the disconnect occurred and increase the virtual memory by the corresponding amount. Reconnect to the instrument and restart the scan. 2. After using a barcode to define the scan protocol with an autoloader instrument in manual mode, the client software may use data contained in the barcode for subsequent scans that do not use barcodes. To work-around this problem, restart the client software before scanning without barcodes. 3. When acquiring images in manual mode, the Job File will not be updated with the experiment information if the Auto-Save images checkbox has not been checked in the protocol file. To work-around this problem, always check the checkbox. 4. When running ABAR in manual mode, the lasers to be used in the protocol should be fully warmed up to avoid inaccurate data. A warning message will be shown when one or more lasers are warming up. However, if the laser(s) to be used are off and no other laser is in warmup, the message is not displayed. The work-around for this problem is to make sure that the laser(s) to be used are turned on prior to running ABAR. 5. Occasionally, on autoloader instruments, the autoloader controller goes into a busy state from which it never returns. The first symptom of this is receiving an autoloader command response timeout error. When this error occurs repeatedly, open the front door to determine if the broken interlock status is recognized on the "Ready" LED. If the broken interlock status is seen, proceed as usual. If the broken interlock status is not seen, restart the instrument and client software. 6. When a user edits an acquisition protocol from within the Acquisition Protocol Editor and renames the protocol via the "Save As" button, the original protocol will also be updated, in memory, with the changes. To revert back to the original protocol, exit ScanArray and restart the application. The original protocol will have returned to its original state. To avoid this problem, it is suggested to rename the protocol via "Save As" prior to making the changes. 7. When the ABAR process (running in manual mode) is cancelled during an external laser fluorophore, a problem will occur the next time that ABAR is run. An error (error code 21600600) indicating that ABAR was commanded to stop will appear. To continue, click OK and repeat the previous step. The process will continue normally. 8. When the autoloader door is opened during a cassette verification operation, multiple problems occur. First, a reject will occur. When the reject message box OK is clicked, focus will not be returned to the Batch Sets dialog. To return focus to the dialog, select the ScanArray application from the Windows taskbar. When focus has returned, the dialog will remain disabled. Hit Esc on the keyboard to exit the dialog. The user may continue with the batch acquisition as normal. It should be noted that while these problems are occurring, the instrument is continuing with the cassette verification and the user should wait for the busy LED on the instrument panel to turn off before attempting to acquire the batch set.