task_ist_preprocessing/src/methods_segmentation/bidcell/config.vsh.yaml at 4b6f566f1048f5bec5d59eaaa6877ef42d81837a · openproblems-bio/task_ist_preprocessing · GitHub

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name: bidcell
label: "BIDCell Segmentation"
summary: "Cell segmentation using BIDCell deep learning approach"
description: "BIDCell is a deep learning method for cell segmentation in spatial transcriptomics data that uses both morphology and transcript information."
links:
  documentation: "https://github.com/SydneyBioX/BIDCell"
  repository: "https://github.com/SydneyBioX/BIDCell"
references:
  doi: "10.1038/s41467-023-44560-w"

__merge__: /src/api/comp_method_segmentation.yaml

arguments:
  - name: --input_scrnaseq_reference
    __merge__: /src/api/file_scrnaseq_reference.yaml
    required: false
    direction: input
  - name: --temp
    type: string
    default: "./temp_bidcell/"
    description: "Temporary directory for BIDCell intermediate files"
  - name: --max_overlaps_pos
    type: integer
    default: 4
    description: "Maximum number of cell types that can share a positive marker"
  - name: --max_overlaps_neg
    type: integer
    default: 15
    description: "Maximum number of cell types that can share a negative marker"
  - name: --model_epochs
    type: integer
    default: 10
    description: "Number of training epochs for BIDCell model"
  - name: --min_cell_size
    type: integer
    default: 15
    description: "Minimum cell size in pixels"

resources:
  - type: python_script
    path: script.py

runners:
  - type: executable
  - type: nextflow
    directives:
      label: [ midtime, lowcpu, highmem, gpu ]

engines:
  - type: docker
    image: openproblems/base_python:1
    setup:
      - type: apt
        packages:
            - libgl1
            - libgl1-mesa-dri
            - libglib2.0-0
            - libsm6
            - libxext6
            - libfontconfig1
            - libxrender1
            - build-essential
            - git

      - type: python
        pip:  scikit-image
      - type: python
        pypi: tifffile
      - type: python
        pypi: natsort
      - type: python
        pypi: opencv-python-headless
      - type: python
        pypi: imgaug
      - type: python
        pypi: matplotlib
      - type: python
        pypi: pandas
      - type: python
        pypi: scikit-learn
      - type: python
        pypi: tqdm
      - type: python
        pypi: pyyaml
      - type: python
        pypi: cellpose==3.1.1.2
      - type: python
        pypi: bidcell
      - type: python
        pypi: spatialdata
      - type: python
        pypi: scanpy
      - type: python
        pypi: dask[dataframe]
      - type: python
        pypi: spatialdata-plot
      - type: python
        pypi: numpy >=1.24.4,<2.0.0
    __merge__:
      - /src/base/setup_txsim_partial.yaml
  - type: native