Quantitative Pathology & BioImage Analysis: QuPath - [NEUBIASAcademy@Home] Webinar
Channel: NEUBIAS
Date: 2020-05-04

Materials and Slides
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See https://qupath.readthedocs.io for further information about downloading public images.

Thanks for those who made images available, including:
- OpenSlide freely-distributable test data (CMU-1, CMU-2, CMU-3, OS-1, OS-2, OS-3)
- La Jolla Institute for Immunology and Moores Cancer Center (Human tumor, Ki67.Pos.Brain, Pancreas Insulin)
- Perkin Elmer, CC BY 4.0 (LuCa-7color)
- Image Data Resource - see https://idr.openmicroscopy.org/webclient/img_detail/9798441/?dataset=10151
- Dr Yvonne Dombrowski (Mid timepoint)

Video Outline:
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Start of Presentation: 1:04
Acknowledgements: 10:20
QuPath hands on: 10:39
Color Deconvolution in QuPath: 15:53
Projects in QuPath: 18:29
Managing Project Entries: 20:29
QA I - Extras staining colors: 24:03
QuPath Annotations: 27:15
Cell Detection in QuPath: 32:41
Sending Images to ImageJ: 34:57
QA II - Omero Integration: 38:30
Full cell detection and classification workflow: 40:49
QA III: Exporting Heatmaps to ImageJ: 51:20
Pixel Classifier: 53:36
Simple Threshold Classifier: 1:02:53
View multiple images in parallel: 1:05:51
Transfer & Transform nnotations: 1:07:49
Distance Metrics: 1:08:50
Multiclass annotations on multiplex images: 1:11:40
Better nuclei detection with StarDist: 1:16:58
QA IV: 1:22:55 

Contents:
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QuPath is open source software that offers a distinctive new approach to bioimage analysis. It has been designed to handle awkward images that are not supported by other popular open source tools – including whole slide and highly-multiplexed data. However, QuPath’s extensive features (including a hierarchical data model, interactive machine learning for pixel and object classification, powerful annotation and visualization tools, scripting support, integration with OpenCV and ImageJ… and much more) make it suitable for a wide range of applications, including fluorescence microscopy.
This webinar is both for new and experienced QuPath users, as well as curious biologists and bioimage analysts who want to see what it can do. Focuses on the latest features included in the just-updated v0.2.0, not covered in the YouTube tutorials at https://www.youtube.com/c/qupath. So even if you think you know the software, there is a lot that’s new!

Speakers:
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Author and Speaker: Peter Bankhead is a Senior lecturer at the University of Edinburgh, creator of QuPath and author of 'Analyzing fluorescence microscopy images with ImageJ'.

Moderators:
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Melvin Gelbard has a background in computer science, bioimage analysis and AI, and now co-develops QuPath with Pete at the University of Edinburgh.
Dr. Laura Murphy is a bioimage analyst in the core light microscopy facility in the Institute of Genetics and Molecular Medicine in Edinburgh.
Ofra Golani is a bioimage analyst at Weizmann Institute


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All Questions & Answers are available here, where you can further ask questions in the future:

https://forum.image.sc/t/neubias-academy-home-webinar-quantitative-pathology-bioimage-analysis-qupath-questions-answers/37387


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