I am using CellProfiler to analyse black speckles on cropped regions of brightfield colour images. I manage to put together a pipeline to count the area of the cropped image, and the area of the black speckles within this cropped image. I am experiencing several problems:
- threshold out of 0-1 range in PrimAutomatic module: will this affect my results?
- PrimManual seems to display the stretched image by default, even if I select raw image subsequently.
- Calculations: I would like to divide the areas of the dots by the area of the cropped object. is there such a module within CellProfiler?
- Units of area: my cropped images are all of different sizes, but are analysed using the same pipeline: are their original dimensions retained? I would like to make comparisons across the cropped images, so it is crucial that they have not been scaled differently.
- When the cropped object is small, CellProfiler identifies the edges of the image as the black speckles (which appear white, because I have converted the image to grayscale and inverted it) even when there are really no dots at the edges, and when I have chosen to discard objects which touch the border of the image in the identifyPrimAutomatic module.
I have attached my pipelines for your reference: one crops the images and calculate area of the cropped image, the other analyses the speckles. I split it into two to reduce the time I have to spend in front of the computer to wait for CellProfiler to analyse the images after each one is cropped. If you know how I can crop multiple images all at once, and then do the subsequent analysis all on CellProfiler, I would be very happy to hear your suggestion!
Thanks very much for your help! I think CellProfiler is an amazing program. : )
countspeckleareaPIPE.mat (1.23 KB)
CropimagesPIPE.mat (1.04 KB)