Step-by-step analysis walkthrough#
This section provides a detailed, step-by-step demonstration of the preprocessing, analysis, and handling of individual samples in single-cell spatial transcriptomics data using InSituPy. Each part of the tutorial builds upon the previous one, and it is recommended to follow the steps sequentially from top to bottom to ensure proper functionality.
Tutorial showing how to use the automated image registration pipeline to register histological stainings or IF stainings performed on the same slide as the scST assay.
Tutorial with introduction into first steps of analysis including filtering, preprocessing and dimensionality reduction.
InSituPyTutorial introducing how to import annotations and regions from external sources like QuPath or add them in the napari viewer.
Tutorial showing how to crop data.
Tutorial showing different options to perform cell type annotation.
Demonstration on how to explore gene expression along an axis of the dataset.