Hello, I’ve been trying out your software and I think it would be great for my particular application however I was hoping that I could get some help.
What we are investigating is if cells or other objects adhere to a particular coating. The coating is printed into circular features in a microarray design. We are dealing with thousands of features in a single analysis which is why CellProfiler’s automated analysis would be useful.
The sort of pipeline that I’d like to use would be something as described below:
Open images (bright field and other channels for single circular feature)
Crop/Mask circular feature in bright field
Apply Crop/Mask to other channels
Count cells inside and outside Crop/Mask
Repeat for all images
The problems arise due to variability in the images and the circular feature. The feature is roughly circular, roughly in the centre, can vary in size (from 400-1000um), and can have faint borders. Also due to the large number of images it would not be ideal for manual input to be involved for every image.
If someone could suggest a way to tackle this it would be very much appreciated. If it helps I can include some example images if requested.