![]() ![]() Generating the tissue annotation can be a little tricky, for fluorescent images I started sending a downsampled image to ImageJ and using blur+thresholding tools there to generate the initial annotation. I've been enjoying the book you made on fluorescent image analysis as well. PS thank you so much for all your efforts. I've resorted to just using Photoshop and manually counting, but that's a huge pain.ĬellProfiler looks like it might have some cool features, and I presented the problem there too:īut could some combination of QuPath + Cell Profiler (or QuPath alone) get the job done? I feel like it can. I've tried to use Fiji and I still don't know how to do this in a straight forward way. This is such a core analysis for a lot of neuroscience. Optional for ISH: Count puncta inside of cells.Sometimes this will be binary (yes/no) but it'd be nice to make more bins like absent, low, medium and high. Count the overlapping events: I want to see which cells have combinations of fluorescent signals: red alone, red+green, green alone, etc.Identify the cellular staining: Usually, cells have (DAPI) and then one or more IHC signals (antibody) or ISH signal (RNAscope, which usually show as puncta).But counting and finding overlaps, that is the part that I need to automate. I'm willing to draw ROIs by hand or some combination of auto-detect plus clean-up by hand.Identify cells in spinal cord tissue sections, either automatically or by manually.QuPath looks like it could be an extremely useful tool for a standard analysis I do. ![]()
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