scimap.pl.image_viewer

Short description

This function spins up a napari instance to view an image. For large images, it is advised to load only a few markers at a time by using the markers parameter. Any categorical data stored in adata.obs can also be overlayed on the image using the overlay parameter.

Parameters

image_path : string
Location to the image file.

seg_mask: string (The default is None)
Location to the segmentation mask file.

adata : AnnData object

overlay : string, optional (The default is None)
Name of the column with any categorical data such as phenotypes or clusters.

overlay_category : list, optional (The default is None)
If only specfic categories within the overlay column is needed, pass their names as a list. If None, all categories will be used.

markers : list, optional (The default is None)
Markers to be included. If none, all markers will be displayed.

imageid : string, optional (The default is imageid)
Column name of the column containing the image id.

subset : string, optional (The default is None)
imageid of a single image to be subsetted for analyis. Only useful when multiple images are being analyzed together.

channel_names : list, optional (The default is adata.uns['all_markers'])
List of channels in the image in the exact order as image.

x_coordinate : string, optional (The default is 'X_centroid')
X axis coordinate column name in AnnData object.

y_coordinate : string, optional (The default is 'Y_centroid')
Y axis coordinate column name in AnnData object.

point_size : int, optional (The default is 10)
point size in the napari plot.

point_color : string, optional (The default is None)
Pass a color that should be used for the overlayed points. e.g. white. By default, a random color is chosen for each layer.

**kwargs : None
Other arguments that can be passed to napari viewer.

Returns

napari image viewer loads the image.

Example

image_path = '/Users/aj/Desktop/ptcl_tma/image.tif'
sm.pl.image_viewer (image_path, adata, overlay='phenotype',overlay_category=None,
            markers=['CD31','CD19','CD45','CD163','FOXP3'],
            point_size=7, point_color='white')