The Color Map plugin allows a user to overlay an intensity map over a whole slide image (WSI). In particular, this is useful for the visual representation of cellularity or 2D probability distributions. The intensity map is displayed with a violet (low) to red (high) color scale (the "jet" scale in OpenCV). The color scale is normalized between the lowest and highest pixel values in the intensity map. The user can set a percent transparency value that determines how the color map is displayed, and can choose whether to display the color map with or without the underlying slide image.
The intensity map file must be a greyscale image in .jpg format. Before running, the view must be zoomed out so that the entire low-resolution slide image is contained within the view area. When the intensity map is loaded, the horizontal and vertical dimensions of the slide image are used to scale the horizontal and vertical dimensions of the intensity map's JPEG image. If the dimensions of the imported file are not in the same ratio as the dimensions of the whole slide image, unexpected stretching or shrinking of the intensity map may result.
1. Open a whole-slide image (WSI) in Sedeen Viewer. Zoom out so that the whole image is displayed within the view area.
3. Adjust the Transparency slider or enter a number between 0 and 100 in the spinbox to choose how the intensity map will be displayed.
4. To display only the color map and hide the slide image, check the box labeled, "Display color map only". Leave this unchecked to overlay the color map over the slide image.
6. Click the Run button to display the intensity map. Two examples of the output are shown below. Fig. 3 shows the result of setting transparency to 40% and choosing to display the whole slide image (unchecking the Display color map only box). Fig. 4 shows the result of setting the transparency to 0%.
Color Map Plugin was developed by Azadeh Yazanpanah with contributions by Michael Schumaker, Martel lab at Sunnybrook Research Institute (SRI), University of Toronto and was partially funded by NIH grant.
Copyright (c) 2019 Sunnybrook Research Institute
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