Add WSI support - #239
Draft
dmoore247 wants to merge 7 commits into
Draft
Conversation
Creating code checkpoint. Testing completed end to end run. VLM did not find phi though.
using openslide, add support for all wsi types. Support at this time includes ingest, indexing, phi detection. Fine tuning PHI pixel detection.
`make style` invoked `pre-commit` from PATH, which pyenv shims intercepted since it's only installed in `.venv/`. Same for the hooks' `language: system` entries (black, isort, autoflake). Prepend `.venv/bin` to PATH and call the venv's pre-commit explicitly. Applies the resulting reformats. Co-authored-by: Isaac
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Ingest .svs, .tiff, .tif, ... file types supported by open slide
Extract metadata, common and vendor specific into the
metacolumnImplement VLMDetector