Xenium Analysis Tools

A Python library for processing and analyzing Xenium sections, utilizing SpatialData formatting.

In Code Ocean Package Manager:

pip: git+[https://github.com/AllenInstitute/xenium_analysis_tools#egg=xenium-analysis-tools]

• To get updated version of package, need to 'refresh' package image - usually removing and adding again works.

---

params.json

Configurations for processing (folder/file names, MapMyCells parameters, options for functions, etc.)

Modules

1. process_xenium

Tools for processing raw Xenium outputs, managing SpatialData objects, and preparing data for downstream analysis.

Main processing functions:

• generate_dataset_slides: Generate the slide-level SpatialData objects from Xenium bundles for a Xenium dataset.
• process_dataset_slides: Generate the section-level SpatialData objects from slides for a Xenium dataset.

Task-specific functions:

• process_spatialdata: Functions for processing/formatting Xenium SpatialData objects.
• divide_sections: Functions for dividing multi-section slides into individual sections w/independent coordinate systems.
• validate_sections: Quality control checks to ensure section processed correctly.

2. map_xenium

Tools for mapping cell types to Xenium data using reference taxonomies.

Main processing function:

• map_dataset_sections: Map multiple sections in a dataset using MapMyCells.
• map_sections: Functions for mapping cell types for an individual section.

3. utils

Shared utility functions used across the library.

• io_utils: Functions for loading data/organizing slides/sections, etc.

CO Capsules

generate_xenium_spatialdata

• Runs generate_dataset_slides

process_xenium_spatialdata

• Runs process_dataset_slides

map_xenium_types

• Runs map_dataset_sections

xenium_analysis_capsule

• Capsule with notebooks for examples of how to work with SpatialData objects, explanations of processing steps, plotting, etc.

xenium_alignment

• Use landmarks to find affine transforms and align data modalities

xenium_napari_spatialdata

• View aligned sections in Napari