Pixel Classifiers

Sara McArdle demonstrates how to use pixel classifiers to measure areas and create objects.
Files drive.google.c... and a related presentation docs.google.co... are available for download.
00:26 Picosirius Red Fast Green holiday cheer!
01:03 Introduction to the slide by Ken Kim
05:08 Setting deconvolution vectors
06:10 A tool is just a tool...
06:30 Making a classifier to get tissue annotations
07:34 The importance of correct image exposure settings for easier analysis
07:56 Creating objects from the classifier
10:05 Edge effects in some files
11:26 Question: How can we manually split annotations?
12:16 New tool in 0.5 - split annotations by line
12:48 Using thresholder to measure collagen in regions
17:52 Saving the classifier
18:34 Measuring collagen content within annotations
21:22 Question: Why there are 2 measurements for the collagen area?
21:55 Question: how to automate this across many slides?
22:50 Introduction to Alcian Blue - Periodic Acid Schiff stain on the intestinal Swiss roll
25:16 Manual stain deconvolution
28:03 Monitor calibration is important when working with colors
29:22 Using polyline tool to train pixel classifier
32:13 The quality and variety of training data is important
33:30 Train pixel classifier window
34:10 Adjusting features used by the classifier
36:48 Visualizing the features used by the classifier
40:50 Switching the live prediction off for slower computers
41:05 Creating detections from the pixel classifier
42:27 Recreating objects with a smaller minimum size
If you have any questions about the videos or the training course, please ask on this image.sc forum post. forum.image.sc...
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Please follow this document to get everything you need (software, files, cheat sheets, and additional resources):
docs.google.co...