Cell classification
Channel: Zbigniew Mikulski
Date: 12/11/2023

Sara McArdle presents how to train an object classifier. 
Files https://drive.google.com/drive/folders/1T9g4ex3TFVVCkZ7PdPl9w_61ySakUndI and a related presentation https://docs.google.com/presentation/d/1Nj3_rtBjWYfmEcLEy7Y72BiFQHrrkrE9 are available for download.  

00:00 Cell classification workflow
00:06 Introduction to Lung1 HE image by Ken Kim
04:16 Doing stain deconvolution
06:14 Inspecting residual channel
06:59 Starting cell detection
07:27 Adjusting cell visualization
07:54 Fine-tuning cell detection
08:40 Need help? Ask a pathologist!
09:25 Using context help
09:58 Doing cell detection on the whole section
11:02 Adding measurements
11:37 Measuring textures in cells
12:13 Adding smoothed features
12:58 The order of adding features is important
13:59 Adding annotations for the classifier
16:09 Working with the Object classifier
18:24 Improving the classifier
20:17 Balancing the training set
21:49 Saving your training data for future
23:05 Starting with a clean slate
24:10 Training an eosinophil classifier
24:35 Using the points tool for annotating rare training objects
28:38 Examples of eosinophils and false-positives
32:01 The importance of not confusing the classifier
33:10 Hiding unclassified objects
34:24 Different classifier algorithms
35:20 Calculate variable importance
37:02 Changing the features used for training
40:42 Training the classifier across different images
43:29 How to deal with classifying different objects
43:58 How to classify non-cellular objects?

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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