My better third is struggling with some microscopy data, counting cells, and I thought: surely there is a computer program that can do this for her. So I started poking around and I found Cell Profiler. I went through the tutorials, and I created a pipeline based on one of her images. Her is a zip file with the image and the pipeline (findingdots.cp):
If you look at the image, the black dots represent the cells she is trying to count. I started mucking around with the different options in the ‘identifyprimaryobjects’ module. Quite frankly the number of options and the different combination are a little daunting, and I was wondering if someone with more experience could provide me with some advice on how to go forward.
Both my better third and I would surely appreciate it.