Cellprofiler is exactly what I need!
grayscale tissue autofluorescence microscopy images
I want to:
- quantify cell and nuclear change of intensity, size, shape, crowding (hallmarks of cancer)
- export into Excel for plotting and comparison between normal and abnormal tissue
- determine the nuclear differences between regions of interest within a single image (ex1 attached)
- determine the nuclear differences within an individual image (ex2 attached)
- compare different images (for example, quantify difference between ex1 and ex2)
I successfully ran the Speckles pipeline using the two default images. When I tried to apply only one image, ex1 (image attached):
- I had to convert to .tif from .jpg
- the output access file was empty
- the output data images were blank (white screen)
- error occurred:
“There was a problem running the analysis module IdentifyPrimAutomatic which is number 07. Error using ==> CPthreshold at 206 Image processing was canceled in the IdentifyPrimAutomatic module because you have chosen to calculate the threshold on a per-object basis, but CellProfiler could not find the image of the objects you want to use.”
What format do my images need to be in? (RGB, .tif, etc.?) I did get grayscale .jpg to work, but only after putting it in a separate file.
Do I need two images for comparison?
What is the difference between the default 1-162hrh2ax2.tif and 1-162hrhoe2.tif? Are they Green and Blue components?
Are the Tissue Neighbors and Speckle pipelines the most appropriate for what I am trying to do?
Are there mapping capabilities from the original image to exported data? That is, once exported to excel, how do I identify certain regions? (for example, left vs. right in the first uploaded image)
I am just starting with this and am already stuck. Any suggestions would be greatly appreciated, thank you!