Spheroid RGB Statistic Plugin for ImageJ
This Plugin is developed for ImageJ or Fiji.
Input:
RGB image of double or triple stained confocal image of an cancer spheroid.
Output:
Spheroid RGB will take selected Regions of Interest and selected Color Channels to run over each ROI the following statistics:
- Image:
- counted cells marked with dots
- All regions of interest (ROI) from ROI Manager
- Table (optional):
- number of cells of of selected channel and selected ROI
- threshold mean intensity of selected channel and selected ROI
- mean intensity of the peaks which representing the nuclei
- area of selected channel and selected ROI (number of pixels within threshold)
- total area measurement of the ROI with calibration from source image
- integrated density of selected channel and selected ROI (mean * area)
- ratio values between channels (count, peak mean, mean, area)
- ratio mean of each pixel value: mean of the ratio per pixel
Example output "Count an Mean" with the red and blue channel selected (major channel blue):
| Image | ROI | count (blue) | peaks mean (blue) | mean (blue) | area (blue) | integrated density (blue) | count (red) | peaks mean (red) | mean (red) | area (red) | integrated density (red) | total area (pixel) | total area (mm) | count ratio | peaks mean ratio | mean ratio | area fraction | ratio mean |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EdU.tif | 0294-0255 | 403 | 128.94 | 48.396 | 98956 | 4789109 | 193 | 130.969 | 27.152 | 67998 | 1846250 | 98956 | 33018.352 | 0.479 | 1.016 | 2.706 | 0.687 | 0.42 |
- Multi Plot:
- plot the average intensity of multiple profiles through the centroid of the spheroid (selected area)
- maximum coordinates of average plot
- bounds related to the gradient of the plot
- area under the plotted channel to major channel bounds
Example output "Multi Plot" with the red and blue channel selected (major channel blue):
| Plot | red max x | red max y | red bounds x | red bounds y | blue max x | blue max y | blue bounds x | blue bounds y | red area (blue bounds) | blue area (blue bounds) |
|---|---|---|---|---|---|---|---|---|---|---|
| Plot SN33267.tif | 245 | 206.76 | 536 | 9.468 | 496 | 207.161 | 641 | 7.918 | 67875.963 | 60766.86 |
Started from template minimal Maven project implementing an ImageJ 1.x plugin.
Cell counting based on the algorithm from the ITCN Plugin, which is looking for local intensity peaks in 8-bit images. Center for Bio-Image Informatics, University of California
Spheroid RGB was developed for the Auckland Cancer Society Research Center.