Vizgen · Example Payload

Vizgen Watershed_Default

CompanySpatial BiologySpatial TranscriptomicsGenomicsLife SciencesBioinformaticsSingle Cell AnalysisScientific InstrumentsOpen SourceCommand Line Tools

Vizgen Watershed_Default is an example object payload from Vizgen, with 4 top-level fields. It illustrates the shape of data this provider's APIs accept or return.

Top-level fields

experiment_propertiessegmentation_taskssegmentation_task_fusionoutput_files

Example Payload

{
  "experiment_properties": {
    "all_z_indexes": [0, 1, 2, 3, 4, 5, 6],
    "z_positions_um": [1.5, 3, 4.5, 6, 7.5, 9, 10.5]
  },
  "segmentation_tasks": [
    {
      "task_id": 0,
      "segmentation_family": "watershed",
      "entity_types_detected": [
        "cell"
      ],
      "z_layers": [
        0, 1, 2, 3, 4, 5, 6
      ],
      "segmentation_properties": {
        "model_dimensions": "2D"
      },
      "segmentation_parameters": {
        "stardist_model": "2D_versatile_fluo",
        "seed_channel": "DAPI",
        "entity_fill_channel": "PolyT"
      },
      "polygon_parameters": {
        "simplification_tol": 2,
        "smoothing_radius": 3,
        "minimum_final_area": 100
      },
      "task_input_data": [
        {
          "image_channel": "DAPI",
          "image_preprocessing": []
        },
        {
          "image_channel": "PolyT",
          "image_preprocessing": [
            {
              "name": "blur",
              "parameters": {
                "type": "gaussian",
                "size": 21
              }
            }
          ]
        }
      ]
    }
  ],
  "segmentation_task_fusion": {
    "entity_fusion_strategy": "harmonize",
    "fused_polygon_postprocessing_parameters": {
      "min_distance_between_entities": 1,
      "min_final_area": 500
    }
  },
  "output_files": [
    {
      "entity_types_output": [
        "cell"
      ],
      "files": {
        "run_on_tile_dir": "result_tiles",
        "mosaic_geometry_file": "watershed_mosaic_space.parquet",
        "micron_geometry_file": "watershed_micron_space.parquet",
        "cell_metadata_file": "watershed_cell_metadata.csv"
      }
    }
  ]
}