Repository navigation
Apposed Cellcast - #320
Draft
gnodar01 wants to merge 12 commits into
Draft
Apposed Cellcast#320gnodar01 wants to merge 12 commits into
gnodar01 wants to merge 12 commits into
Conversation
- create appose/napari env - launch nepari and transfer image on run - don't ignore src
This reverts commit 03107d7. It works but not quite ready for production use
This reverts commit 1433f93. It worked, but we don't actually want pixelshuffel as an apposed plugin it was just for testing viability
- Make worker script single function entrypoint with model dispatch - Refactor to allow for keeping the environment alive and the model within it warm, across execution cycles
gnodar01
added this pull request to stack #321
October 9, 2026 02:17
- In order to use import_library feature, not yet published
- Wrap cellcast worker in import_library - Simplifies caching logic by avoiding use of globals() - Allows persisting plain variables across tasks within the imported library
This branch has not been deployed
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
This PR builds on #239 by adding the apposed RunCellCast plugin. This plugin runs in an appose environment and therefore relies on CellProfiler/CellProfiler#5203. It uses cellcast to provide Stardist2D (H&E + fluo) and Stardist3D (fluo) models running on GPU regardless of platform (via webGPU). It also allows for custom weight files.
In general it forms the basis of officially supported, apposed plugins, capable of running plugins that require extra dependencies (even from .app/.exe variants of CellProfiler), without the user needing to manually set up the environments.