I am an undergraduate student who is looking at cell shape changes in certain cells. I have a program that easily finds cell outlines and creates a color image of the cell shapes. However, when I try the Identify Primary Images in my Cell Profiler pipeline, it is only able to detect some of the cells. I have fiddled with different threshold strategies to no avail. I have attached the image I have been using and I have included the pipeline that I have created. Any suggestions would be appreciated!
You could attempt to 1) turn it to grayscale, 2) enhance edges and 3) invert the resulting image (you could also create a binary image from this). This would (in theory) give you a bright foreground with dark seperating lines.
There might be a way simpler method that I just don’t know of!
Thank you so much! It worked perfectly. You are a lifesaver.
@Fabba123 , I was wondering if CP can identify primary objects on a color image and also insert the outlines? I saw this software http://www.mipar.us/ in action and it does exactly that…check this out https://drive.google.com/folderview?id=0B6nj1d7RmQ7TLVBTX1FvNmhMU1U&usp=sharing
I’m sure CP can do something similar but I don’t know how to make it do it. Any help/suggestion will be highly appreciated.
It is possible! I would highly suggest you take a look at the example pipelines, and the helpful manual. CP is a powerful tool if you appreciate its functions.