API

Import Stereopy :

import stereo as st

• IO: io

The io module includes input and output parts.

The input part supports reading files in multiple formats to generate StereoExpData object, such as GEM, GEF, H5ad (from Scanpy and Seurat) and so on. In addition, we provide the conversion function between StereoExpData and AnnData so that swithing between tools would be smoother. In output part, we support writing StereoExpData as H5ad file for storage.

• StPipeline: tl

A tool-integrated class for basic analysis of StereoExpData, which is compromised of basic preprocessing, embedding, clustering, and so on.

• Plots: plt

Here supports both static and interactive plotting modes to visualize our analysis results vividly.

• Image: im

The module works on image files, generating results of tissue or cell segmentation that you are interested in.

• Tools: tools

The module helps correct cell segmentation and generates corresponding CGEF file after cell cutting.

• Utils: utils

The module handles with multiple batches of data.