AllenCell/allencell-segmenter-ml

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Napari plugin for ml segmentation

Stars: 5
Forks: 3
Open beginner issues: 0
Indexed issues: 171

Dominant language: Python
License: No license data
Last GitHub push: Sep 22, 2025
Latest indexed: Sep 13, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Open All

171 open issues indexed

Determine remote GPU feasability Open

AllenCell/allencell-segmenter-ml#11 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Run napari from Ubuntu EC2 instance Open

blocked

AllenCell/allencell-segmenter-ml#86 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Napari integration test Open

AllenCell/allencell-segmenter-ml#100 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
cyto-dl client integration tests Open

AllenCell/allencell-segmenter-ml#162 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Create way to download sample data from cyto-dl for users Open

AllenCell/allencell-segmenter-ml#170 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Enable publish workflow to edit itself to list current version Open

AllenCell/allencell-segmenter-ml#190 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Improve handling of napari viewer events in prediction Open

AllenCell/allencell-segmenter-ml#201 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Move I/O operations to worker threads Open

AllenCell/allencell-segmenter-ml#204 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Explore alternative solutions for channel extraction multithreading Open

low priority refactor

AllenCell/allencell-segmenter-ml#205 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Fix workflow file issues with deployment Open

AllenCell/allencell-segmenter-ml#210 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Refactor prediction checklist to avoid thread interrupts Open

AllenCell/allencell-segmenter-ml#218 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Disable structure size/image dimension inputs when continuing training Open

low priority

AllenCell/allencell-segmenter-ml#221 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Curation UI blocks while loader initializes Open

AllenCell/allencell-segmenter-ml#223 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Support all types of training inputs Open

wontfix

AllenCell/allencell-segmenter-ml#225 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Curation save csv button Open

🚨 high priority🚨

AllenCell/allencell-segmenter-ml#227 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Curation requirement experiment name Open

duplicate wontfix

AllenCell/allencell-segmenter-ml#229 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Test using pyside Open

🚨 high priority🚨

AllenCell/allencell-segmenter-ml#230 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Refactor: move all module-level methods into Classes as staticmethods Open

low priority refactor

AllenCell/allencell-segmenter-ml#231 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Use cyto-dl overrides manager to generate overrides for prediction Open

low priority refactor

AllenCell/allencell-segmenter-ml#234 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Single curation mask layer Open

🚨 high priority🚨 bug

AllenCell/allencell-segmenter-ml#248 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
test cyto-dl latest fixes Open

🚨 high priority🚨

AllenCell/allencell-segmenter-ml#250 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Reorder the module tabs Open

medium priority UI/UX

AllenCell/allencell-segmenter-ml#255 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Update the model selection section's text Open

medium priority UI/UX

AllenCell/allencell-segmenter-ml#256 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Curation UI: Update Progress section Open

🚨 high priority🚨 UI/UX

AllenCell/allencell-segmenter-ml#261 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Enable [+Create] button for Excluding Mask Open

🚨 high priority🚨 needs clarification UI/UX

AllenCell/allencell-segmenter-ml#262 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Curation UI: set colormap & blending mode for images loaded in the viewer by the Curation UI Open

🚨 high priority🚨 UI/UX

AllenCell/allencell-segmenter-ml#263 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Curation UI: Add feedback message at the end of the curation Open

🚨 high priority🚨 UI/UX

AllenCell/allencell-segmenter-ml#265 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Curation UI: load only structure channel in the raw image if the image is a multi-channel file Open

needs clarification UI/UX

AllenCell/allencell-segmenter-ml#266 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Curation UI: Behaviors related to [Delete] mask button click Open

medium priority needs clarification UI/UX

AllenCell/allencell-segmenter-ml#267 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Bug: Curation UI: [raw] image loaded incorrectly Open

bug needs clarification UI/UX

AllenCell/allencell-segmenter-ml#268 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Curation UI: Mask section updates Open

medium priority UI/UX

AllenCell/allencell-segmenter-ml#269 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
UX: Curation UI: Make [Save] mask button more prominent Open

UI/UX

AllenCell/allencell-segmenter-ml#270 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 13, 2026
Curation UI: Design: Add [Save Progress] function to save out CSV Open

medium priority UI/UX

AllenCell/allencell-segmenter-ml#271 · 4 comments · 0 reactions · 2 assignees · Indexed Sep 13, 2026
Training UI: Update Training Images section Open

medium priority UI/UX

AllenCell/allencell-segmenter-ml#272 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 13, 2026
UX: Training UI: Display model stats upon training completion Open

low priority UI/UX

AllenCell/allencell-segmenter-ml#273 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Prediction UI: Remove Pre/Post Processing section Open

🚨 high priority🚨 UI/UX

AllenCell/allencell-segmenter-ml#274 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
UI/UX: Update text throughout the plugin Open

🚨 high priority🚨 UI/UX

AllenCell/allencell-segmenter-ml#275 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
TBD: Display result images from Prediction UI for on-screen image Open

medium priority UI/UX

AllenCell/allencell-segmenter-ml#276 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
UX: Test if models are platform dependent Open

AllenCell/allencell-segmenter-ml#277 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 13, 2026
Remove Channel Selection from Training & Curation UI for V1 Open

UI/UX

AllenCell/allencell-segmenter-ml#278 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Model Selection: Show/Hide tab modules depends on the user's selection Open

🚨 high priority🚨 UI/UX

AllenCell/allencell-segmenter-ml#279 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Curation UI: add a warning if user closes the plugin Open

medium priority UI/UX

AllenCell/allencell-segmenter-ml#280 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Curation: generate test and validation csv Open

🚨 high priority🚨 needs clarification

AllenCell/allencell-segmenter-ml#281 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Training UI: warning message for CSV input Open

needs prioritization UI/UX

AllenCell/allencell-segmenter-ml#282 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 13, 2026
Catch-all notes only Open

AllenCell/allencell-segmenter-ml#284 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Thao share training dataset w Brian Open

AllenCell/allencell-segmenter-ml#285 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Main screen: update disabled/hidden tabs state if a model has not been selected Open

🚨 high priority🚨 UI/UX

AllenCell/allencell-segmenter-ml#286 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 13, 2026
Training requires filters override Open

🚨 high priority🚨

AllenCell/allencell-segmenter-ml#289 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Set num workers based on users # of available cores on cpu Open

medium priority

AllenCell/allencell-segmenter-ml#290 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 13, 2026
Curation record list changed directly in model state Open

low priority refactor

AllenCell/allencell-segmenter-ml#295 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 13, 2026

AllenCell/allencell-segmenter-ml

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