task_ist_preprocessing/src/methods_segmentation/watershed/config.vsh.yaml at bfddcba01aa3c88f859fdde277d9611f55f9b232 · openproblems-bio/task_ist_preprocessing · GitHub

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name: watershed
label: "watershed Segmentation"
summary: "Output of the segmentation method watershed"
description: "Output of the segmentation method watershed"
links:
  documentation: "https://github.com/openproblems-bio/task_ist_preprocessing"
  repository: "https://github.com/theislab/txsim"
references:
  doi: "10.1109/34.87344"


__merge__: /src/api/comp_method_segmentation.yaml

arguments:
- name: --normalize_func
  type: string
  default: "gamma"
- name: --normalize_gamma
  type: integer
  default: 1
- name: --normalize_gain
  type: integer
  default: 1
- name: --normalize_inv
  type: boolean
  default: False
- name: --normalize_cutoff
  type: double
  default: 0.5
- name: --contrast_adjustment_func
  type: string
  default: "equalize_adapthist"
- name: --contrast_adjustment_kernel_size
  type: string
  default: "None"
- name: --contrast_adjustment_clip_limit
  type: double
  default: 0.01
- name: --contrast_adjustment_nbins
  type: integer
  default: 256
- name: --contrast_adjustment_mask
  type: string
  default: "None"
- name: --contrast_adjustment_in_range
  type: string
  default: "image"
- name: --contrast_adjustment_out_range
  type: string
  default: "dtype"
- name: --blur_func
  type: string
  default: "gaussian"
- name: --blur_sigma
  type: integer
  default: 1
- name: --blur_output
  type: string
  default: "None"
- name: --blur_mode
  type: string
  default: "nearest"
- name: --blur_cval
  type: double
  default: 0.0
- name: --blur_preserve_range
  type: boolean
  default: False
- name: --blur_truncate #keep as double
  type: double
  default: 4.0
- name: --threshold_func
  type: string
  default: "local_otsu"
- name: --threshold_nbins
  type: integer
  default: 256
- name: --threshold_hist
  type: string
  default: "None"
- name: --threshold_out
  type: string
  default: "None"
- name: --threshold_mask
  type: string
  default: "None"
- name: --threshold_shift_x
  type: boolean
  default: False
- name: --threshold_shift_y
  type: boolean
  default: False
- name: --threshold_shift_z
  type: boolean
  default: False
- name: --threshold_footprint
  type: string
  default: "square"
- name: --threshold_footprint_size
  type: integer
  default: 50
- name: --distance_transform_func
  type: string
  default: "distance_transform_edt"
- name: --distance_transform_sampling
  type: string
  default: "None"
- name: --distance_transform_return_distances
  type: boolean
  default: True
- name: --distance_transform_return_indices
  type: boolean
  default: False
- name: --distance_transform_distances
  type: string
  default: "None"
- name: --distance_transform_indices
  type: string
  default: "None"
- name: --local_maxima_func
  type: string
  default: "find_local_maxima"
- name: --local_maxima_min_distance
  type: integer
  default: 5
- name: --post_processing_func_1
  type: string
  default: "remove_small_objects"
- name: --post_processing_min_size_1
  type: integer
  default: 64
- name: --post_processing_connectivity_1
  type: integer
  default: 1
- name: --post_processing_out_1
  type: string
  default: "None"
- name: --post_processing_func_2
  type: string
  default: "remove_small_holes"
- name: --post_processing_area_threshold_2
  type: integer
  default: 64
- name: --post_processing_connectivity_2
  type: integer
  default: 1
- name: --post_processing_out_2
  type: string
  default: "None"
- name: --bg_intensity_filter_bg_factor
  type: double
  default: 0.3
- name: --bg_intensity_filter_window_size
  type: integer
  default: 1000
- name: --bg_intensity_filter_bg_size
  type: integer
  default: 2000

resources:
  - type: python_script
    path: script.py

engines:
  - type: docker
    image: openproblems/base_python:1
    __merge__:
      - /src/base/setup_txsim_partial.yaml
      - /src/base/setup_spatialdata_partial.yaml
  - type: native

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