QuPath Workshop From Samples to Knowledge 2020 - Day 1

Get the files here: http://tiny.cc/filestograb 5:55 Introduction to QuPath - Pete Bankhead 35:30 How to use QuPath like a pro - Zbigniew Mikulski 3:00:45 Tips on how to get help with open source software - Pete Bankhead 3:06:15 The art of finding answers and asking questions - Mike Nelson 3:15:45 Using pixel classifier to measure areas - Zbigniew Mikulski, Matthew Meyer, and Mike Nelson 4:31:25 New Features in QuPath - Pete Bankhead This is a live recording from our workshop and a lot of sessions have longish breaks when we were helping our participants. You can skip to more relevant parts using links below. Using QuPath like a pro: 35:28 Setting up preferences and memory 37:40 Creating a project, adding images 44:50 Exploring the controls 50:37 Hold space bar to move 51:20 Image type, stain deconvolution 53:35 One key to rule them all, Ctrl/Cmd+L 55:20 Estimate stain vectors 57:25 All images have artifacts 1:00:25 Rotate images, add a new class and start annotating 1:07:40 Getting your measurements 1:09:05 Observe multiple images with multi-view feature 1:11:00 Wand tool 1:15:04 Introduction to working with fluorescence images 1:17:45 Brightness & contrast, working with channels 1:25:20 Be color friendly! 1:26:48 Know your artifacts 1:33:12 Fixation is key to your success 1:43:30 Trick to rename channels quickly 1:52:00 Simple measurements 1:59:00 Export measurements and snapshots 2:02:02 Simple tissue detection 2:10:50 Getting it all together and making your first script 2:14:40 Cell detection on brightfield image 2:22:30 Training cell detection classifier 2:27:24 Creating project training image 2:31:15 Notes on making a better classifier Pixel classifier: 3:43:24 Using multi-view to learn about artifacts by comparing modalities; see the video in original quality here https://youtu.be/ZsoBzLMmZF8 4:20:00 Focus problems will affect your classification; see the video in original quality here https://youtu.be/_lGPKjivfyU Thank you for watching and... 4:10 Thank you to all who helped with this workshop! Get the files here: http://tiny.cc/filestograb and make sure to fill out the evaluation form There is a slight shift between the video and sound, sorry about that! :)