synapse-net/synapse_net/napari.yaml at 38b1a2c3bd1cafb2df7ab2db165f23824212995d · computational-cell-analytics/synapse-net · GitHub

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name: synapse_net
display_name: SynapseNet

# See https://napari.org/stable/plugins/manifest.html for valid categories.
categories: ["Image Processing", "Annotation"]

contributions:
  commands:
    # Commands for widgets.
    - id: synapse_net.segment
      python_name: synapse_net.tools.segmentation_widget:SegmentationWidget
      title: Segmentation
    - id: synapse_net.distance_measure
      python_name: synapse_net.tools.distance_measure_widget:DistanceMeasureWidget
      title: Distance Measurement
    - id: synapse_net.file_reader
      title: Read volumetric data
      python_name: synapse_net.tools.volume_reader:get_reader
    - id: synapse_net.morphology
      python_name: synapse_net.tools.morphology_widget:MorphologyWidget
      title: Morphology Analysis
    - id: synapse_net.vesicle_pooling
      python_name: synapse_net.tools.vesicle_pool_widget:VesiclePoolWidget
      title: Pool Assignment
    - id: synapse_net.postprocessing
      python_name: synapse_net.tools.postprocessing_widget:PostprocessingWidget
      title: Segmentation Postprocessing

    # Commands for sample data.
    - id: synapse_net.sample_data_tem_2d
      python_name: synapse_net.sample_data:sample_data_tem_2d
      title: Load TEM 2D sample data
    - id: synapse_net.sample_data_tem_tomo
      python_name: synapse_net.sample_data:sample_data_tem_tomo
      title: Load TEM Tomo sample data
    - id: synapse_net.sample_data_tomo_small
      python_name: synapse_net.sample_data:sample_data_tomo_small
      title: Load small tomo sample data
    - id: synapse_net.sample_data_mito_small
      python_name: synapse_net.sample_data:sample_data_mito_small
      title: Load TEM Tomo sample data

  readers:
    - command: synapse_net.file_reader
      filename_patterns:
      - '*.mrc'
      - '*.rec'
      - '*.h5'
      accepts_directories: false

  widgets:
    - command: synapse_net.segment
      display_name: Segmentation
    - command: synapse_net.distance_measure
      display_name: Distance Measurement
    - command: synapse_net.morphology
      display_name: Morphology Analysis
    - command: synapse_net.vesicle_pooling
      display_name: Pool Assignment
    - command: synapse_net.postprocessing
      display_name: Segmentation Postprocessing

  sample_data:
    - command: synapse_net.sample_data_tem_2d
      display_name: TEM 2D Sample Data
      key: synapse-net-tem-2d
    - command: synapse_net.sample_data_tem_tomo
      display_name: TEM Tomo Sample Data
      key: synapse-net-tem-tomo
    - command: synapse_net.sample_data_tomo_small
      display_name: Small Tomo Sample Data
      key: synapse-net-tomo-small
    - command: synapse_net.sample_data_mito_small
      display_name: Small Mito Sample Data
      key: synapse-net-mito-small