Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
img
 
 
jar
 
 
 
 
 
 
 
 
 
 

Spheroid RGB Statistic Plugin for ImageJ

This Plugin is developed for ImageJ or Fiji.

GUI demo

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.

About

ImageJ Plugin to count cells from an rgb image and other usefull statistics

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages