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Feature/all cells mask segmentation#633

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BrianWhitneyAI wants to merge 11 commits intomainfrom
feature/all-cells-mask-segmentation
Open

Feature/all cells mask segmentation#633
BrianWhitneyAI wants to merge 11 commits intomainfrom
feature/all-cells-mask-segmentation

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@BrianWhitneyAI BrianWhitneyAI commented Jan 8, 2026

Context

The purpose of this PR is to create a POC for AICS compute pipelines. It resolves #702 It is NOT intended to be merged. The goal of this design is to deliver something that people can try out so that we can verify interest in this project and identify more requirements from the user’s side. The proof of concept is limited to running “All Cells Mask” on central IT’s Slurm cluster.

Demo

Heres a demo of the feature. The video was too large to embed
https://drive.google.com/file/d/1a2FQpDDN_wR4q_2TuYaZ4SP9AxZOecW3/view?usp=sharing

Development notes.

  1. The waiting states for the CSV are very fragile and hacky they should definitely not be merged, they are included to smooth over the POC.
  2. This pipeline currently requires files to have local vast paths, I would recommend removing that complexity if we decide to move this into a real feature
  3. theres no process failure error support currently and minimal response error handling

Build

This feature is Desktop only so heres the build if you want to try it out!
https://github.com/AllenInstitute/biofile-finder/actions/runs/20826578098

Comment thread packages/core/components/Modal/AllCellsMaskSegmentation/index.tsx Outdated
Comment thread packages/core/state/interaction/logics.ts Outdated
Comment thread packages/core/services/FileService/HttpFileService/index.ts Outdated
Comment thread packages/desktop/src/services/DatabaseServiceElectron.ts Outdated
Comment thread packages/core/hooks/useProcessFilesMenuItems.ts Outdated
Comment thread packages/core/services/FileService/HttpFileService/index.ts Outdated
@BrianWhitneyAI BrianWhitneyAI force-pushed the feature/all-cells-mask-segmentation branch from f9f3239 to 37e223a Compare March 25, 2026 00:00
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Screenshot 2026-03-25 at 12 25 16 PM

const submitDisabled = status !== "idle" || hasNonLocalFiles;

const submitTooltip = hasNonLocalFiles
? "All selected files must be available locally before submitting this job."
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I'm wondering if we should match the wording here with the wording on the copy to vast option for files. E.g. 'All selected files must be copied to the VAST cache before submitting this job')

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Feature Request: Bff to Compute - ACM1 pipeline

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