addROI_omero
Short Description
sm.hl.addROI_omero
: The function allows users to add annotations that have been
extracted from Omero using the following
script: https://gist.github.com/Yu-AnChen/58754f960ccd540e307ed991bc6901b0.
Function
addROI_omero(adata, roi, x_coordinate='X_centroid', y_coordinate='Y_centroid', imageid='imageid', subset=None, overwrite=True, label='ROI', n_jobs=-1, verbose=False)
Parameters:
Name | Type | Description | Default |
---|---|---|---|
adata |
AnnData object |
required | |
roi |
DataFrame
|
Pandas dataframe of ROI's that have been extracted from Omero using the following script: https://gist.github.com/Yu-AnChen/58754f960ccd540e307ed991bc6901b0. Please note that the function currently does not handle overlapping ROI's and so make sure the ROI's are mutually exclusive. |
required |
x_coordinate |
float
|
Column name containing the x-coordinates values. |
'X_centroid'
|
y_coordinate |
float
|
Column name containing the y-coordinates values. |
'Y_centroid'
|
imageid |
string
|
In the event that the adata object contains multiple images, it is
important that ROIs are added to each image seperately. Pass the name
of the column that contains the |
'imageid'
|
subset |
list
|
Name of the image to which the ROI is to be added. Note if you have multiple images in the adata object, you will need to add ROI's to each image one after the other independently. |
None
|
overwrite |
bool
|
In the event you have multiple images in the adata object, ROI can be added to each image
independently using the |
True
|
label |
string
|
Key for the returned data, stored in |
'ROI'
|
n_jobs |
int
|
Number of cores to use. Default is to use all available cores. |
-1
|
Returns:
Type | Description |
---|---|
adata
Modified AnnData object. Check |
1 2 |
|
Source code in scimap/helpers/_addROI_omero.py
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