Vizgen · Example Payload
Vizgen Cellpose_Default_1_Zlevel
CompanySpatial BiologySpatial TranscriptomicsGenomicsLife SciencesBioinformaticsSingle Cell AnalysisScientific InstrumentsOpen SourceCommand Line Tools
Vizgen Cellpose_Default_1_Zlevel 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": "Cellpose",
"entity_types_detected": [
"cell"
],
"z_layers": [
3
],
"segmentation_properties": {
"model": "cyto2",
"model_dimensions": "2D",
"custom_weights": null,
"version": "latest"
},
"task_input_data": [
{
"image_channel": "PolyT",
"image_preprocessing": [
{
"name": "normalize",
"parameters": {
"type": "CLAHE",
"clip_limit": 0.01,
"filter_size": [
100,
100
]
}
}
]
},
{
"image_channel": "DAPI",
"image_preprocessing": [
{
"name": "normalize",
"parameters": {
"type": "CLAHE",
"clip_limit": 0.01,
"filter_size": [
100,
100
]
}
}
]
}
],
"segmentation_parameters": {
"nuclear_channel": "DAPI",
"entity_fill_channel": "PolyT",
"diameter": 70,
"flow_threshold": 0.95,
"mask_threshold": -5.5,
"minimum_mask_size": 500
},
"polygon_parameters": {
"simplification_tol": 2,
"smoothing_radius": 10,
"minimum_final_area": 500
}
},
{
"task_id": 1,
"segmentation_family": "Cellpose",
"entity_types_detected": [
"cell"
],
"z_layers": [
3
],
"segmentation_properties": {
"model": "nuclei",
"model_dimensions": "2D",
"custom_weights": null,
"version": "latest"
},
"task_input_data": [
{
"image_channel": "DAPI",
"image_preprocessing": [
{
"name": "normalize",
"parameters": {
"type": "CLAHE",
"clip_limit": 0.01,
"filter_size": [
100,
100
]
}
}
]
}
],
"segmentation_parameters": {
"nuclear_channel": "DAPI",
"entity_fill_channel": null,
"diameter": 55,
"flow_threshold": 0.8,
"mask_threshold": -3,
"minimum_mask_size": 500
},
"polygon_parameters": {
"simplification_tol": 2,
"smoothing_radius": 10,
"minimum_final_area": 500
}
}
],
"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": "cellpose_mosaic_space.parquet",
"micron_geometry_file": "cellpose_micron_space.parquet",
"cell_metadata_file": "cellpose_cell_metadata.csv"
}
}
]
}