spateo.preprocessing.image#
Image preprocessing.
Module Contents#
Functions#
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Preprocessing of an image. Remove background with the global threshold. Pixel intensity is set to 0, for all the |
- spateo.preprocessing.image.remove_background(adata: anndata.AnnData, threshold: float | str = 'auto', slice: str | None = None, used_img_layer: str | None = None, return_img_layer: str | None = None, inplace: bool = False, show: bool = True) anndata.AnnData | None[source]#
Preprocessing of an image. Remove background with the global threshold. Pixel intensity is set to 0, for all the pixels intensity, less than the threshold value. If the threshold is not provided, it will be calculated by OSTU’s method.
- Parameters:
- adata
AnnData object.
- threshold
Global threshold used. If the threshold is not provided, it will be calculated by OSTU’s method.
- slice
Name of the slice.
- used_img_layer
Name of used image layer.
- return_img_layer
Name of output image layer.
- inplace
Perform computation inplace or return result.
- show
Show the preprocessed image or not.
- Returns:
AnnData.uns[‘spatial’][slice][‘images’][return_img_layer]The preprocessed image
AnnData.uns[‘spatial’][slice][‘scalefactors’][return_img_layer]The scale factor for the spots