How to make the warning screen about clipped pixels disappear?

What operating system does ArrayVision FAST require?

Is there a server version of ArrayVision FAST?

What does ArrayVision FAST offer?

Does ArrayVision FAST read different image file formats?

Does ArrayVision FAST have auto-alignment capability?

Can ArrayVision FAST correct for the presence of dust particles and other artifacts in the spot signal?

What does ArrayVision FAST measure?

What other kind of calculations does ArrayVision FAST perform?

Does ArrayVision FAST allow for background correction?

I am having trouble removing my license authorization, what should I do?

How do I create a new protocol?

Can ArrayVision FAST read TIFF files?

I loaded a TIFF image file for analysis. Why is the background intensity higher than the spot intensity?

What can I do if I have dust artifacts in my arrays?

How do I define replicates?

Can I import spot labels?

What is the difference between 'Levels' and 'ROD'?

How can I get a multi-fluor fusion image for my array?

My auto alignment failed. What parameters should I adjust?

I want to use a protocol defined by another user. What should I do?

When I use my wheel mouse, the middle-button function no longer works properly. However, the function still works.

Can the program locate spots with "donut" or other deformed morphologies?

Is it possible to see data from individual pixels?

• Windows NT^® 4.0 (Workstation or Server edition, Service Pack 6 or later) or Windows 2000^® (Professional or Server edition).
• PC compatible computer with a Pentium^® microprocessor.
• High-resolution graphics display (at least 1024 X 768 X 24 bits)
• At least 256 MB RAM

Rapid and automated analysis for array images.
Supports wide variety of image formats.
Configurable templates.
No restriction on array layout or size.
Automated alignment.
Automated dust and artifact correction.
Assessment of spot quality.
Comprehensive normalization and background corrections.
Flexible data reporting and exporting

- MCID (*.im)
- Molecular Dynamics GEL (*.gel)
- BRS (*.img)
- Packard (*.tif)
- TIFF (*.tif)
- MD Dataset (*.ds)
- Fujix BAS Series (*.inf)

ArrayVision FAST can align templates to arrays automatically. ArrayVision FAST Version 6.0 incorporates major improvements and new algorithms for complete "walk-away" auto- alignment of fluorescent arrays. The new alignment will:

- Find the array without the need for manual positioning of the template.
- Calculate array rotation for accurate template positioning.
- Locate any sub-arrays even if they are not positioned correctly as result of misalignment or rotation.
- Align each spot to accommodate variations in spot positions.

Yes, ArrayVision FAST uses statistical thresholds to detect the presence of artifacts in the spot signal. These outlier pixels can be excluded from the analysis or replaced with interpolated values.

ArrayVision FAST reports spot intensity in several ways:
- Mean of all pixels
- Median of all pixels
- Total (mean x area)
- Mean after outlier pixels removed
- Total after outlier pixels replaced.

Background corrected intensity

Yes, ArrayVision FAST allows for background correction that is fully under the user's control:
- Local area surrounding the spot
- Local areas at the corner of each spot
- Selected spots as negative control
- User defined areas around the array

Please turn to your start up-guide for all license authorization questions

The analysis protocol contains essential information about the type of array, the type of analysis, and the destination of the output data. There are two ways to define a new protocol:

1. Use the Protocol Wizard. The Protocol Wizard can be accessed either from the Analysis Wizard (Analysis protocol panel >New) or the Protocol Manager (New icon).
2. Use the Protocol Editor (File > New protocol).

Yes, but exercise caution when analyzing .tif files. .tif files contain raw gray-level information only, and the gray-level scale may not be linearly related to the signal intensity of the specimen. If the relationship is not linear, the gray-level scale is not suitable for expressing relative data values (i.e., for calculating ratios). Inquire from the scanner manufacturer whether this relationship is linear. If it isn't, contact S&S technical Assistance:

TIFF files contain raw gray-level information only. The gray-level scale is, however, a 'brightness' scale and therefore darker image pixels have lower values than lighter ones.

To invert the gray-level scale, you must invert the image. Go to the Transform window (in Advanced mode) and select Inversion from the list of Point Operators. The inversion process will create an image with light spots on a dark background, the brighter the spot, the higher its gray-level value. If you are bothered by the appearance of the inverted image, press the F2 key until the image has dark spots on a light background. This will not affect the inverted image data.

Dust particles can generate signal artifacts, particularly in fluorescent arrays. These artifacts typically demonstrate themselves as extraordinarily bright pixels within a spot. In ArrayVision FAST these artifacts can be detected and removed by selecting the ARM Density or the AR Volume measure in the protocol. ARM Density reports the density value for each spot after first removing pixels with density values that exceed a user-defined threshold. The threshold is defined in terms of median absolute deviations (MADs) above the median (default value is 4.0). The AR Volume uses a similar, threshold-based procedure to detect and replace artifact pixels. It differs from ARM density in that it reports volume (the density value for each spot multiplied by its area), after first replacing removed pixels values with estimated values. The estimated values are derived by interpolation from neighboring pixels.

In ArrayVision FAST, any spots or groups of spots that are given the same name are considered replicates. In the Data Table, replicates are distinguished by automatically giving them a suffix [(a), (b), etc.]. Replication patterns can also be indicated during protocol definitions in the Protocol Editor. In the Labels panel of the Protocol Editor, click Edit and then click on the Replication Pattern icon ().

Yes, you can import text or Excel label files. The label file can be constructed either as a spreadsheet, mirroring the array structure or as a list of names that the program allocates to spots based on a defined pattern. To import labels in the protocol editor, select Use gene names and click Import in the Labels panel.

Gray levels (Levels) are the raw pixel intensity values upon which all other density/intensity scales are based. When a phosphor plate or fluorescence scanner scans a specimen, luminescence data are obtained as voltages read from a photomultiplier. The voltage measurements are mapped into discrete gray levels and are then stored in an image file. Most scanners convert the initial gray-level values to other, user-friendlier density/intensity units (e.g., Relative Fluorescence Units, Counts). The end result is a scale that is linearly related to the signal concentration in the original specimen, and more suited to a fluorescent or radioisotopic label. All digital images are comprised of 2 x levels, where x is the bit density of the image file. A 16-bit image, for example, contains 216 = 65,536 levels, where black pixels = 0 and white pixels = 65,535. Gray-level values 1-65,534 represent the varying shades of gray between black and white. Relative Optical Density (ROD) is an Imaging Research Inc. proprietary density scale. It is an inverse logarithmic function of gray-level values, and should only be used with radioisotopic arrays that have been exposed to X-ray film and digitized with a camera. Since the ROD scale is logarithmic, it is not suitable for expressing relative values (i.e., for calculating ratios).

ArrayVision FAST will allow you to view a composite image of two or three different fluor-scan images of an array (e.g. cy3 and cy5). To construct and view the fusion image, first retrieve the two images and then click on the Arrays menu and select More. Select Multiple fluor fusion and adjust the visuals. Select red, green, or blue coloration for the parent images. Press Apply to view the composite image.

If auto-alignment (Fluorescent Method) fails or does not produce satisfactory results, experiment with adjusting the following parameters:
- Increase the size of the spot area in layout (if possible).
- Adjust the positioning of the template (indicated by the green border) to account for any array warping or rotation.

To use a protocol supplied by another user you need to import it into ArrayVision FAST. You can import protocols in the Protocol Manager (Import icon). In the Protocol Manager you can also export a protocol for sharing with another user (Export icon).

Download and install the current version of MouseWare from the Logitech Web site (www.logitech.com), even if you are using a Microsoft Intellimouse. Once the driver has been installed, open the Mouse settings dialog. Change the setting for button 2 to be "Middle Button". Once this is done, the mouse will function properly. No other setting for button 2 will function properly in ArrayVision FAST.

There are several morphometric measures available that can be used to analyze spot morphology. These measures are normally hidden and need to be activated. If you would like to perform morphometric analysis of your arrays, please contact S&S for activation instructions.

Yes, it is possible to report the values of all the pixels in a spot. For more information, please contact S&S Bioscience technical Assistant at:

In the U.S.A./Canada & South America	Europe/Africa & Asia
techserv@schleicher-schuell.com (800) 245-4024, option 3	techbio@schleicher-schuell.de 49 5561 791 676