since it has been a while since I posted on this forum, I open a new thread. The old one can be found here:
Again, thanks a lot for all that input. I worked a lot on my pipeline and also had to make some changes to my actual experimental setup. Since I had big issues with Antibody-staining as well es Autoflourescence on human vascular smooth muscle cells, I switched to VSMC from GFP-mice, which work well for what I am doing.
I build a more advanced pipeline, already generated about 600 Gigabyte of Image Data and I am almost ready to analyze them I just got a little issue with exporting statistics. Since I cannot fully analyze my pictures automatically, I use the Cellprofiler to filter potential events, sort out those images and export a modified version of the picture that I can easily and fast double check. However, I will need the total number of “VSMCNuclei” and potentially “MacNuclei” as well, so I can do the statistics later and determine the percentage of positive events compareds to the total count of VSMC. Right now, I have a spreadsheet which gives this data by counting the rows of entries. However, I will have hundreds of thousands of cells and I wondered if there is a simple solution that can give me the total number of the desired cells after each run (which consists of about 1200 images).
I got another thing that would still be able to improve my pipeline: Is there a way to make those objects (VSMCNucleiUnfiltered) become “MacNuclei” that are filtered in step 7? (All VSMCs that are too bright are most likely to be big Macrophages, so I would rather treat them as those instead of deleting them from the picture. It will not affect the total count a lot, but if one can do that, it’d be great.
I included a zip file with 5 test images as well as the pipeline and would appreciate any help.
Thx and best regards,
Roeper - CP - 20110802.zip (9.11 MB)