image_viewer
Short Description
sm.pl.image_viewer
: The function allows users to open OME-TIFF images inside
Napari and overlay any any categorical column such as cluster annotation or phenotypes.
Function
image_viewer(image_path, adata, overlay=None, flip_y=True, overlay_category=None, markers=None, channel_names='default', x_coordinate='X_centroid', y_coordinate='Y_centroid', point_size=10, point_color=None, subset=None, imageid='imageid', seg_mask=None, **kwargs)
Parameters:
Name | Type | Description | Default |
---|---|---|---|
image_path |
str
|
Location to the image file (TIFF, OME.TIFF, ZARR supported) |
required |
seg_mask |
str
|
Location to the segmentation mask file. |
None
|
adata |
Ann Data Object
|
|
required |
flip_y |
bool
|
Flip the Y-axis if needed. Some algorithms output the XY with the Y-coordinates flipped.
If the image overlays do not align to the cells, try again by setting this to |
True
|
overlay |
str
|
Name of the column with any categorical data such as phenotypes or clusters. |
None
|
overlay_category |
list
|
If only specfic categories within the overlay column is needed, pass their names as a list. If None, all categories will be used. |
None
|
markers |
list
|
Markers to be included. If none, all markers will be displayed. |
None
|
channel_names |
list
|
List of channels in the image in the exact order as image. The default is |
'default'
|
x_coordinate |
str
|
X axis coordinate column name in AnnData object. |
'X_centroid'
|
y_coordinate |
str
|
Y axis coordinate column name in AnnData object. |
'Y_centroid'
|
point_size |
int
|
point size in the napari plot. |
10
|
point_color |
str, dict
|
The default behavior is to assign auto colors, but you can also provide
a color mapping using the point_color parameter. For instance, you can pass a
dictionary that maps color values to specific categories (provided in the |
None
|
imageid |
str
|
Column name of the column containing the image id. |
'imageid'
|
subset |
str
|
imageid of a single image to be subsetted for analyis. Only useful when multiple images are being analyzed together. |
None
|
Returns:
Type | Description |
---|---|
Napari Viewer (image viewer): |
1 2 3 4 |
|
Source code in scimap/plotting/_image_viewer.py
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