io.convert_ROI_table_to_indices
io.convert_ROI_table_to_indices(ROI, pxl_sizes_zyx, cols_xyz_pos=['x_micrometer', 'y_micrometer', 'z_micrometer'], cols_xyz_len=['len_x_micrometer', 'len_y_micrometer', 'len_z_micrometer'])
Convert physical units in region-of-interest tables (ROI) to indices based on the given scale level.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
ROI |
Name of the region of interest | required | |
pxl_sizes_zyx |
Physical size of the zyx pixels in units given defined in multiscales (usually um) | required | |
cols_xyz_pos |
Name of columns identifying the xyz positions | ['x_micrometer', 'y_micrometer', 'z_micrometer'] |
|
cols_xyz_len |
Name of columns identifying the physical dimensions in xyz | ['len_x_micrometer', 'len_y_micrometer', 'len_z_micrometer'] |
Returns
| Type | Description |
|---|---|
| dict[str, int] | A dictionary with FOV names as keys and a list of starting and end pixel indices as [s_z, e_z, s_y, e_y, s_x, e_x]. |
Examples
>>> ROI_table = ad.read_zarr("plate.zarr/C/3/0/tables/FOV_ROI_table/")
>>> operetta_compose.io.convert_ROI_table_to_indices(ROI_table, [1.0, 1.195, 1.195])