Subcellular detections in QuPath are a convenient way of analyzing in-situ hybridization data. Sara McArdle explains how to use them for the analysis of RNAscope data.
00:00:00 Sara McArdle explains how to use subcellular detections in QuPath
00:04:26 Subcellular detections
00:03:39 Creating full image annotation and detecting cells
00:04:55 Setting up detection thresholds
00:06:16 Adjusting detection parameters
00:07:52 Splitting clusters by shape and intensity
00:09:20 Estimated number of spots
00:10:18 Running spot detection on all cells
00:10:55 Trick: use - to temporarily disable spot detection
Files https://drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI and a related presentation https://docs.google.com/presentation/d/11DXEzkogx1VkySzJePG1ChrXPEM_SvWc are available for download.
If you have any questions about the videos or the training course, please ask on this image.sc forum post. https://forum.image.sc/t/qupath-training-course-from-samples-to-knowledge-2023-is-available-online/88618
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Please follow this document to get everything you need (software, files, cheat sheets, and additional resources):
https://docs.google.com/document/d/1VyPtSbvnUC3EWnCVSRmFgFnhsXNHfOkAxOVyhkpYn8I
