I have just started using CellProfiler and I want to do a very specific analysis. After a search in the forum I was able to find a pipeline that does a small part of what I wanted it to do and which I think is a good start point. I tried to combine it with some modules from a different pipeline to make the rest of the analysis I wanted, but there are still some problems that I can’t solve and other things I wanted it to do, but have no idea how. I would appreciate any tips on what modules might do what I want and what is currently wrong with what I am using.
So, ideally, I wanted the program to be able to identify the cells, and measure the fluorescence of each individual cell. Currently what it does is to identify the cells, but it considers the total of the image as one object and thus measures the intensity of all the cells there and not cell by cell, which is what I wanted it to do. Moreover, I keep getting the same error whenever I try to analyze several images (I send a print screen of the error in attachment). I can ignore the error and the analysis will proceed, but it is still annoying to have to click it every single time.
There are still some issues with cells detection, which I assume depend on a more appropriate tuning or the detection parameters. As you can see from the pictures, in some cases I lose a lot of information when identifying the cells.
To summarize, I would appreciate any help in knowing if it is possible to make the analysis of the fluorescence cell by cell instead of taking into account all the cells in one image and get those results in an excel file, while also getting back the pictures to make sure I didn’t lose too much information as in the case I show in appendix.
Thanks in advance for all the help!
yeast_cell_fluorescence.cp (5.88 KB)