Bio Image 2D Analyzer
Version 7.0
November 8, 1999

Release Notes

The latest release of Bio Image 2D Analyzer, version 7.0.4, is an extension Version 6.4, designed to significantly decrease the time spent analyzing an image.

New Spotfinding

The new spotfinder uses the same algorithms as the 2-D Analyzer software. However, the user-specified parameters now represent easy-to-determine values. These parameters are used to automatically create several sets of parameters to the original finder. All these sets are run, and the "best" spots selected.

The new parameters are Smallest Spot and Largest Spot, expressed in pixels. You can either enter a number (directly typed or using a slider), or draw a circle around the spot. If you select Mark Spot, you will be prompted to place the mouse in the center of the spot, and drag it to the edge. It is not necessary to get the sizes exactly correct. These sizes determine the set of filter widths to run. The third parameter, Faintest Spot, is now measured in percent over background. For example, if spots must be twice as dark as background, enter 100. As an aid to determining this parameter, the image now displays background in the lower right corner; it is the rightmost of the 4 numbers.

Differences

The enhancement we believe will result in the most significant increase in processing throughput is in the Review module. This is highly automated processing of differences between a new image and an existing composite.

Differences is a new submenu in the Match menu. This submenu has the choices Resolve Differences, Select Saved Differences, and Clear Saved Differences.

Resolve Differences

The Resolve Differences window shows a list of all the images comprising a composite, except the reference image. Along with each image is a count of differences, sorted into five categories:

  • Spots that are 2 or more in the previous images, but only 1 in the new image.
  • Spots that are 1 in the previous images, but 2 or more in the new image.
  • All spots in the new image that are outside the "perimeter" of all spots in the previous images. For example, if you have carefully edited out spots on the gel front of your previous image(s), and not the new image.
  • All spots that are only in the new image (perimeter spots is a subset of this)
  • Spots that are only in the previous images.

You can also choose to sort the differences by descending Integrated Intensity (spot volume), or X/Y Coordinates.

The appropriate Resolve Differences subwindow will appear. Each subwindow has five operations. Perimeter, New, and Previous also have two sliders. All open images have a red box around the spot to be resolved; if there is not a spot on an image, the red box is where the spot would be. The differences are displayed in the Ambiguous Match color; use Change Viewing Options to set this color. After you press one of the operation buttons, it advances to the next difference.

For 2+ in Previous, now 1, the operations are Divide in New, and Combine in Previous. Divide in New will create as many spots in the new image as are present in the previous images. Each will have the correct match number, and the composite will be updated accordingly. This is identical to manually adding spots and quantifying them with Mark Axes. Combine in Previous replaces the several spots in the previous images with one spot, which is the approximate size of the spot in the new image.

For 1 in Previous, now 2+, the operations are Combine in New, and Divide in Previous.

For Perimeter, the operations are Delete from New, and Add to Previous.

For Only in New, the operations are Delete from New, and Add to Previous

For Only in Previous, the operations are Add to New, and Delete from Previous.

All windows have three common operations: Back, Next, and Save.

  • Back moves the red boxes to the previous difference.
  • Next moves the red boxes to the next difference.
  • Save puts the spot onto a saved list, for later manual processing.

Perimeter, Only in New, and Only in Previous have two sliders.

  • The first allows for the appropriate deletion of the lightest X percent of the differences.
  • The second allows for the appropriate addition of the darkest X percent of the differences.

 

 

 

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