task_ist_preprocessing/src/methods_transcript_assignment/rna2seg/config.vsh.yaml at bd36088827697cc5bb5f17517d4299777c4e39d7 · openproblems-bio/task_ist_preprocessing · GitHub

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__merge__: /src/api/comp_method_transcript_assignment.yaml

name: rna2seg
label: "RNA2Seg Transcript Assignment"
summary: "Assign transcripts to cells using the RNA2Seg method"
description: "RNA2seg is a deep learning-based segmentation model designed to improve cell segmentation in Imaging-based Spatial Transcriptomics (IST)."
links:
  documentation: "https://rna2seg.readthedocs.io/en/latest/index.html"
  repository: "https://github.com/fish-quant/rna2seg"
references:
  doi: "10.1101/2025.03.03.641259"

arguments:
  - name: --transcripts_key
    type: string
    description: The key of the transcripts within the points of the spatial data
    default: transcripts

  - name: --coordinate_system
    type: string
    description: The key of the pixel space coordinate system within the spatial data
    default: global

  - name: --flow_threshold
    type: double
    description: Flow threshold for detecting cells
    default: 0.9

  - name: --cellbound_flow_threshold
    type: double
    description: Cell boundary flow threshold for detecting cells
    default: 0.4

  - name: --create_cytoplasm_image
    type: boolean
    description: Whether to create an artificial cytoplasm image based on thresholding the nuclear stain image
    default: False

  - name: --cytoplasm_min_threshold
    type: double
    description: Minimum percentile for cytoplasm image thresholding
    default: 0.25

  - name: --cytoplasm_max_threshold
    type: double
    description: Maximum percentile for cytoplasm image thresholding
    default: 0.75

  - name: patch_width
    type: integer
    description: Size of sopa patches to tile over image for parallelization. May affect segmentation output.
    default: 1000

  - name: patch_overlap
    type: integer
    description: Overlap of sopa patches to tile over image for parallelization.
    default: 50


resources:
  - type: python_script
    path: script.py

engines:
  - type: docker
    image: openproblems/base_python:1
    __merge__:
      - /src/base/setup_spatialdata_partial.yaml
    setup:
      - type: docker
        # env:
        #   - PATH="/root/.cargo/bin:${PATH}"
        run:
          - apt-get update && apt-get install libgl1 -y
      - type: python
        pypi: [rna2seg, "numcodecs==0.15.1"]
  - type: native

runners:
  - type: executable
  - type: nextflow
    directives:
      label: [ hightime, highcpu, midmem ]