Cell Detection and Cell Measurements
Channel: Zbigniew Mikulski
Date: 2023-11-12

Cell Detection and Cell Measurements by Sara McArdle explains one of the most commonly used tools in QuPath. This discusses how to find cells and measure their intensity in brightfield and fluorescence images. 

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.

0:00 Introduction to cell detection in QuPath by Sara McArdle
1:29 Stain deconvolution for brightfield images
3:00 Color deconvolution explained by Mike Nelson
6:05 Cell detection parameters
14:35 Running cell detection on a whole image
15:45 What is the requested pixel size by Pete Bankhead
17:40 Checking the accuracy of cell detection
18:55 Cell detection and default measurements 
19:55 Positive cell detection and setting intensity thresholds
23:57 Working with cell detection in fluorescence images. Introduction by Ken Kim
29:00 Selecting the proper cell detection channel for fluorescence images and adjusting the threshold
32:12 Creating tissue annotation by using the wand tool
34:00 Measurement maps
38:55 Additional measurements (Haralick features) 
41:38 Adding smoothed features
45:30 Preparing for data export
46:52 QuPath hierarchy
48:04 Export measurements for annotations and cell objects
49:30 Calculating cell density

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
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/1VyPtSbvnUC3EWnCVSRmFgFnhsXNHfOkAxOVyhkpYn8I