scimap.hl.add_roi_omero

Short description

Helper function to add ROI's extracted from Omero using this script. Please note that the function currently does not handle overlapping ROI's. Hence please make sure the ROI's are mutually exclusive.

Parameters

adata : AnnData object

roi : data frame, required (The default is None)
Pandas dataframe of ROI's that have been extracted from Omero.

x_coordinate : float, required (The default is 'X_centroid')
Column name containing the x-coordinates values.

y_coordinate : float, required (The default is 'Y_centroid')
Column name containing the y-coordinates values.

label : string, optional (The default is 'ROI')
Key for the returned data, stored in adata.obs.

Returns

Modified AnnData object. Check adata.obs for an additional column.

Example

# Load the ROI CSV file
roi = pd.read_csv('ROI/ROI_Z147_1_750.csv')

# Run the function
adata = sm.hl.add_roi_omero (adata, roi, label='aj_ROI')