scallops.io.to_label_crops

scallops.io.to_label_crops(intensity_image, label_image, objects_df, output_dir, crop_size=(224, 224), output_format='tiff', centroid_cols=None, gaussian_sigma=None)

Export individual label crops as tiff or npy files.

Parameters:

• intensity_image (Array | Array) – Image data

• label_image (Array | Array | None) – Label data. If supplied, image is masked by corresponding segmentation mask

• objects_df (DataFrame) – DataFrame containing objects from find-objects.

• crop_size (tuple[int, int]) – Size of label crop

• output_dir (str) – Crop output directory

• output_format (Literal['tiff', 'npy']) – Crop output format

• centroid_cols (Sequence[str] | None) – Columns in objects_df containing y and x centroids.

• gaussian_sigma (float | None) – If not None, apply gaussian-smoothed mask to isolate target mask

Returns:

Objects dataframe (with objects at well edges removed)

Return type:

DataFrame