tasks.regionprops_measurement
tasks.regionprops_measurement
Functions
| Name | Description |
|---|---|
| feature_table | Generate a regionprobs feature table |
| regionprops_measurement | Take measurements using regionprobs and write the features to the OME-ZARR |
feature_table
tasks.regionprops_measurement.feature_table(labels, img, properties=['label', 'area', 'intensity_mean', 'intensity_max', 'intensity_min', 'eccentricity', 'perimeter', 'centroid', 'solidity'])
Generate a regionprobs feature table
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
labels |
np.ndarray | A labels array | required |
img |
np.ndarray | An intensity array | required |
properties |
list[str] | A list of regionprops properties | ['label', 'area', 'intensity_mean', 'intensity_max', 'intensity_min', 'eccentricity', 'perimeter', 'centroid', 'solidity'] |
Returns
| Type | Description |
|---|---|
| pd.DataFrame | A feature dataframe including a column with the label index |
regionprops_measurement
tasks.regionprops_measurement.regionprops_measurement(zarr_url, table_name='regionprops', label_name='nuclei', level=0, overwrite=False)
Take measurements using regionprobs and write the features to the OME-ZARR
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
zarr_url |
str | Path to an OME-ZARR Image | required |
table_name |
str | Folder name of the measured regionprobs features | 'regionprops' |
label_name |
str | Name of the labels to use for feature measurements | 'nuclei' |
level |
int | Resolution level (0 = full resolution) | 0 |
overwrite |
bool | Whether to overwrite any existing OME-ZARR feature table | False |