Cellpose Options

The Cellpose segmentation algorithm uses the Cellpose v.1.0.2 [citation]. In addition to supporting the default model weights (e.g. cyto2, nuclei), vpt supports custom weights that may be more appropriate for a specific tissue type.

Input Data

The number of channels Cellpose requires is based on the model selected. For the nuclei model, only a nuclear channel is necessary (typically DAPI). For the cyto2 model, both a nuclear and entity fill channel are required.

Cellpose Model Properties

The following model properties are REQUIRED:

  • model ("cyto2" or "nuclei")

  • model_dimensions ("2D" or "3D")

    "2D" applies the 2D Cellpose model to all z-planes specified in the z_layers list seperately and the results are combined into a 3D output. "3D" applies the native-3D Cellpose model to all z-planes specified in the z_layers list.

The following model properties are OPTIONAL:

  • custom_weights (path to a custom Cellpose weights file, local file system only)

  • version (any valid string, used for record keeping)

Usage:

"segmentation_properties": {
  "model": "cyto2",
  "model_dimensions": "2D",
  "custom_weights": null,
  "version": "latest"
},

Cellpose Model Parameters

The following model parameters are required:

  • nuclear_channel (The image channel that represents nuclei)

  • entity_fill_channel (The image channel that either fills or outlines the cells)

  • diameter (typical cell size, pixels)

  • flow_threshold (range: 0 to 1, larger values output more cells)

  • mask_threshold (range: -6 to 6, lower values output larger cells)

  • minimum_mask_size (minimum cell size, pixels)

Detailed descriptions of each parameter are available in the Cellpose documentation

Usage:

"segmentation_parameters": {
    "nuclear_channel": "DAPI",
    "entity_fill_channel": "PolyT",
    "diameter": 70,
    "flow_threshold": 0.95,
    "mask_threshold": -5.5,
    "minimum_mask_size": 500
}
citation

Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature methods, 18(1), 100-106.