task_ist_preprocessing/src/methods_segmentation/cellpose/config.vsh.yaml at b9014f22cf2c9a694c2d3710df1128b52aa9d550 · openproblems-bio/task_ist_preprocessing · GitHub

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name: cellpose
label: "Cellpose Segmentation"
summary: "Output of the segmantation methot cellpose"
description: "Output of the segmantation methot cellpose"
links:
  documentation: "https://github.com/openproblems-bio/task_ist_preprocessing"
  repository: "https://github.com/openproblems-bio/task_ist_preprocessing"
references:
  doi: "10.1038/s41592-020-01018-x"


__merge__: /src/api/comp_method_segmentation.yaml

arguments:
  - name: --batch_size
    type: integer
    default: 8
  - name: --model_type
    type: string
    default: "cyto"
  - name: --resample
    type: boolean
    default: True
  - name: --channel_axis
    type: string
    default: "None"
  - name: --z_axis
    type: string
    default: "None"
  - name: --normalize
    type: boolean
    default: True
  - name: --invert
    type: boolean
    default: False
  - name: --rescale
    type: string
    default: "None"
  - name: --diameter
    type: double
    default: 30.0 #default should be None with cellpose v4
  - name: --do_3D
    type: boolean
    default: False
  - name: --anisotropy
    type: string
    default: "None"
#  - name: --net_avg
#    type: boolean
#    default: False
  - name: --augment
    type: boolean
    default: False
  #- name: --tile
  #  type: boolean
  #  default: True
  - name: --tile_overlap
    type: double
    default: 0.1
  #- name: --interp #Seems to be removed in v4
  #  type: boolean
  #  default: True
  - name: --flow_threshold
    type: double
    default: 0.4
  - name: --cellprob_threshold
    type: double
    default: 0.0
  - name: --min_size
    type: integer
    default: 15
  - name: --stitch_threshold
    type: double
    default: 0.0

resources:
  - type: python_script
    path: script.py

engines:
  - type: docker
    #image: openproblems/base_pytorch_nvidia:1 # TODO: ideally get gpu image to work
    image: openproblems/base_python:1
    setup:
      - type: python
        pypi: cellpose<4.0.0
    __merge__:
      - /src/base/setup_txsim_partial.yaml
      - /src/base/setup_spatialdata_partial.yaml
  - type: native

runners:
  - type: executable
  - type: nextflow
    directives:
      label: [ midtime, midcpu, veryhighmem, gpu ]