Most of the analysis I'm currently doing is along the lines of "percent area positively stained" and "mean intensity of positive stain" but I was hoping there were some good programs for more complex imaging analysis available out there. I would love to do some sort of spacial analysis on my staining.
For example: I am staining tumors and investigating factors that influence tumor immunity so I'd love to be able to do an analysis that shows how often two cell types (identified by my stains) show up in the same area, or how often they associate with each other in space. Or whether certain populations build up on the tumor edge or evenly disperse throughout the tumor.
Is there a good analysis for studying spacial distribution of positive staining? Or anything else interesting for that matter? Just trying to get the most out of my data.
The main software I'm using is ImageScope but have access to Nikons NIS-Elements and obviously any open source programs, I also know how to code in R but have never incorporated that into my staining analysis.
How about CellProfiler?
https://cellprofiler.org
https://github.com/CellProfiler/CellProfiler/wiki#What_if_I_want_to_contribute_to_CellProfiler
Thomas Andl that looks like a great option. I'll check it out. Someone also suggested MosaicIA which I'll look into as well
Article MosaicIA: An ImageJ/Fiji plugin for spatial pattern and inte...
Thanks for the suggestion! I'll report back how it goes.
If you can find a Keyence microscope, they often have image analysis software modules that look like Cellprofiler but are much more convenient to apply. Maybe with a little home-made programming in Python, you can get it to the same level as the commercial variants of image segmentation.
Another commercial solution is Halo (https://indicalab.com/halo/). I have no experience with it nor do I know how pricey it is.
UPENN may have that in some core facility?
Check https://amp-reddit-com.cdn.ampproject.org/wp/s/amp.reddit.com/r/labrats/comments/pc0qio/best_coding_programs_and_software_ifihc_analysis/?usqp=mq331AQKKAFQArABIIACAw%3D%3D
Also check https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096801
Also check this sir.
https://www.nature.com/articles/s41598-021-83858-x
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