This sounds similar to the image sets I am aiming to analyse. Still trying to get my head around the best way to analyse 100+ images from the one slide.
I have a pathway I am quite happy with for looking at nuclear/cytoplasmic translocation and measuring pixel intensity between nuclear and cytoplasmic regions.
I now have a major project which needs me to analyse at least 100 cells per 3 slide/staining conditions for many many patients. This means I have between 70-100 images per slide to combine which will become unwieldy if I have to run each image individually in cellprofiler.
DAPI Vectastain (BLUE "_B")
FITC (Green "_G")
Texas Red (Red "_R")
I can't attach the image type I get direct from the Zeiss Axion because it is in czi format.
Here is a .tif conversion of the 3-colour image:
I can't attach the xml metadata file either that goes with the 3 colour tif
Tried as GIF also:
again I can't attach the xml metadata file either that goes with the 3 colour gif
Cellprofiler AXION PBMC 060815.cpproj (941 KB)
I have been first opening Zeiss Axion images in the free Zen Lite software and converting the 3 colour image into 3 separate colour images identified into their colours with _B, _G and _R
Is there a way to convert three colour images into 3 tif images?
Do I even need to split up the three colour images before loading into cellprofiler pathway? I was under the impression that I had to do this and designed the attached pathway around this.
Split single colour images:
and a second image set:
Any advice or insight would be much appreciated.
University of Queensland