HistomicsTK: An open source python toolkit for web based analysis of dig
summary
HistomicsTK claims an open-source Python toolkit that performs web-based analysis of whole-slide histopathology images (50,000 px tiles, ~7.5 GB, ~1M nuclei per slide) and integrates with a Digital Slide Archive built on Girder. It exposes existing CLI algorithms via an XML spec, packages them as Docker-based modules, and runs distributed processing on server back ends. The demo shows REST endpoints generated from XML, automatic web UI for parameters, and working image viewers and annotation rendering.
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chapters (10)
- 0:00Introduction
- 2:09Histopathology and whole slide imaging
- 7:11Requirements for histopathology tools
- 8:17HistomicsTK and Girder solutions
- 10:01Digital Slide Archive demo
- 12:29HistomicsTK Python toolkit
- 13:34HistomicsTK Girder plugin
- 15:43Exposing modules on web
- 22:54Software process and future
- 24:40Q&A
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