addRoiImage

addRoiImage ¶

addRoiImage(
    imagePath,
    data,
    roi=None,
    outputDir=None,
    show=True,
    returnData=False,
    returnFig=False,
    sdataTable=None,
    **kwargs
)

Attach ROI polygons to the cell table.

scimap's addROI_image opened the raw image in napari and let you draw regions by hand. scimappro takes the polygons as data instead: pass a roi table (the same shape sp.helpers.addROI_omero takes, i.e. an OMERO ROI export) and each cell is labelled by the region it falls in.

With roi=None the table is returned unchanged, which makes the function safe to leave in a pipeline whose ROIs have not been drawn yet.

Note that imagePath is the first parameter here — this is the one function in scimappro where data is not first, because the image is what identifies the ROIs.

Parameters:

Name	Type	Description	Default
`imagePath`	`(str, required)`	Path to the image the ROIs were drawn on. Recorded for provenance; the image is not read.	required
`data`	`(AnnData \| SpatialData \| str, required)`	The cell table. An `AnnData`, a path to an `.h5ad` file, a `SpatialData` object, or a path to a `.zarr` SpatialData store.	required
`roi`	`DataFrame \| str`	ROI polygons to apply, in the OMERO export format. `None` returns the table unchanged.	`None`
`outputDir`	`str`	Directory to write the updated object to. With `None` the object is returned.	`None`
`show`	`bool`	Accepted for signature compatibility with scimap; nothing is drawn.	`True`
`returnData`	`bool`	Return `obs` as a `DataFrame` instead of the object.	`False`
`returnFig`	`bool`	Return `(None, None)` — or `(None, None, obs)` with `returnData` — for callers that unpack a plotting-style return value.	`False`
`sdataTable`	`str`	Which `SpatialData` table to use.	`None`
`**kwargs`	`dict`	Forwarded to `sp.helpers.addROI_omero` when `roi` is given.	`{}`

Returns:

Name	Type	Description
`result`	`AnnData \| SpatialData \| DataFrame \| tuple`	The updated object by default; `obs` with `returnData=True`; a `(None, None)` tuple with `returnFig=True`.

Example

import pandas as pd

roi = pd.read_csv("rois_from_omero.csv")
adata = sp.pl.addRoiImage("registration/image.tif", adata, roi=roi)
sp.pl.spatialScatterPlot(adata, colorBy="ROI", s=3)