omicverse.space.visium_10x_hd_cellpose_gex

omicverse.space.visium_10x_hd_cellpose_gex(adata, obs_key='n_counts_adjusted', log1p=False, mpp=0.3, sigma=5, gex_save_path='stardist/gex_colon.tiff', prob_thresh=0.01, nms_thresh=0.1, gpu=True, buffer=150, **kwargs)[source]

Run expression-image segmentation and map labels back to spatial bins.

Parameters:

  • adata (AnnData) – Visium HD AnnData.

  • obs_key (str, default='n_counts_adjusted') – Observation value used to generate gene-expression image.

  • log1p (bool, default=False) – Whether to log-transform values when generating image.

  • mpp (float, default=0.3) – Microns-per-pixel scale.

  • sigma (int, default=5) – Gaussian smoothing parameter for grid image generation.

  • gex_save_path (str, default='stardist/gex_colon.tiff') – Output path of generated expression image.

  • prob_thresh (float, default=0.01) – StarDist probability threshold.

  • nms_thresh (float, default=0.1) – StarDist non-max-suppression threshold.

  • gpu (bool, default=True) – Whether to use GPU in StarDist inference.

  • buffer (int, default=150) – Crop buffer used for spatial coordinate key.

  • **kwargs – Additional StarDist arguments.

Returns:

Writes labels_gex back into adata.

Return type:

None