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Density maps and Distances

Sara McArdle shows how to use density maps in QuPath for spatial analysis. Files https://drive.google.com/drive/folder... and a related presentation https://docs.google.com/presentation/... are available for download. 01:13 Loading object classifier and applying classification 02:05 Density maps 03:29 Changing density maps visualization 05:46 Saving density map 05:57 Thresholding density map 06:47 Changing the opacity of thresholded density for better accuracy 07:12 Annotations from density maps 08:00 Question: How can you export visualization and calculate the density of cells per annotation? 08:42 Finding hotspots 11:20 Refining annotations 13:04 Running eosinophil classifier on cleaned annotations 13:35 Question: My classifier is missing features 15:01 Measuring cells' distance from annotation 15:41 Visualizing the results with Measurement maps 16:42 Histograms in detections table for distance measurements 17:19 Going back to the basics - tissue analysis is SPATIAL! 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-train... The more information you can include about your question, the more helpful our answers can be. Please follow this document to get everything you need (software, files, cheat sheets, and additional resources): https://docs.google.com/document/d/1V...