InSituPy: A framework for histology-guided, multi-sample analysis of single-cell spatial transcriptomics data

InSituPy is a Python package designed to facilitate the analysis of single-cell spatial transcriptomics data. With InSituPy, you can easily load, visualize, and analyze the data, enabling and simplifying the comprehensive exploration of spatial gene expression patterns within tissue sections and across multiple samples. Currently the analysis is focused on data from the Xenium In Situ methodology but a broader range of reading functions will be implemented in the future.

Latest changes

!!!Warning: This repository is under very active development and it cannot be ruled out that changes might impair backwards compatibility. If you observe any such thing, please feel free to contact us to solve the problem. Thanks!

For the latest developments check out the releases.

Getting started

Overall data structure

A key feature of InSituPy is its hierarchical data structure, centered around the InSituExperiment and InSituData objects:

• InSituData: Represents and manages at the individual sample level. It integrates all modalities of spatial omics datasets, including cellular readouts, cellular boundaries, images, transcripts, regions, and annotations.
• InSituExperiment: Aggregates multiple InSituData instances and links them with associated metadata, enabling cross-sample analysis and organization.

Which integration should I use?

InSituPy ships two complementary integrations: a skill (a static reference any assistant can load, versioned per release) and an MCP server (live introspection against the installed source). Pick by how you work - they cooperate rather than compete.

flowchart LR
    Q{"How are you working?"}

    A["Code agent<br>Claude Code, Codex, Cursor, ..."]
    B["Plain web chat<br>ChatGPT, Claude.ai"]
    C["Want always-current<br>API introspection"]

    A1["pip install insitupy-spatial<br>then: insitupy install-skill"]
    B1["upload the release ZIP<br>or paste llms.txt"]
    C1["add the MCP server<br>uvx insitupy-mcp"]

    R1["insitupy-api skill<br>in your agent's skills dir"]
    R2["insitupy-api skill<br>loaded into the chat"]
    R3["live tools that<br>never go stale"]

    Q --> A
    Q --> B
    Q --> C
    A --> A1
    A1 --> R1
    B --> B1
    B1 --> R2
    C --> C1
    C1 --> R3
    R3 -.->|skill defers to MCP| R1

AI Assistant Integration (Skill)

Easiest option: install the InSituPy skill (insitupy-api). It teaches any AI assistant - a coding agent or plain web chat - the data model, the typical read -> preprocess -> tools -> plot -> save workflow, and where to look for detailed API references, so it writes correct InSituPy code without guessing from memory. No server, no setup beyond installing the package.

• Code agents (Claude Code, Codex, Cursor, ...): after pip install insitupy-spatial, run

  insitupy install-skill
  

  This copies the skill to ./.agents/skills/insitupy-api/ by default; pass --target {claude,codex,cursor} or --path DIR to install elsewhere, and --force to upgrade an existing copy.

• Plain web chat (ChatGPT, Claude.ai, no skill loader): either paste the contents of the repo-root llms.txt (or its raw URL) into the chat/project knowledge, or upload the insitupy-api-<version>.zip asset attached to the latest release.

The skill is versioned and self-upgrading: if it's missing something you expect, check your installed insitupy.__version__ against the skill's stamped version and re-run insitupy install-skill --force (or re-fetch the ZIP/llms.txt) if it's out of date.

If the insitupy MCP server (below) is also available in your session, an agent following the skill will prefer its live tools automatically - the skill is a fallback, not a competing source.

AI Assistant Integration (MCP Server)

For power users who want live, always-current introspection (not just a static reference), InSituPy also ships an MCP server that gives AI assistants live access to the API, source code, and workflow examples. Because it is a standard MCP server (stdio), it works with any MCP-compatible client, such as Claude Desktop, Claude Code, Cursor, Codex, Windsurf, Continue.dev, or Cline. Setup has mainly been exercised with Claude Desktop and Claude Code; if you use it with another client, feedback is welcome.

The easiest way to activate the server in Claude Desktop is to add the following to your claude_desktop_config.json - no separate installation or repository clone required:

{
  "mcpServers": {
    "insitupy": {
      "command": "uvx",
      "args": ["--python", "3.12", "--from", "insitupy-spatial[mcp]", "insitupy-mcp"]
    }
  }
}

uvx (part of uv) handles downloading and running the server automatically in an isolated environment. Install uv first if you haven't already (curl -LsSf https://astral.sh/uv/install.sh | sh on macOS/Linux, or see installation options).

See MCP_TUTORIAL.md for step-by-step setup instructions (Claude Desktop and Codex; other clients use the same stdio command in their own MCP config).

Documentation

For detailed instructions on using InSituPy, refer to the official documentation.

InSituPy works best within Jupyter Lab or Jupyter Notebook sessions. If you are not familiar with these platforms, see the documentation of Project Jupyter.

Installation

Make sure you have Conda installed on your system before proceeding with these steps. If not, you can install Miniconda or Anaconda from https://docs.conda.io/en/latest/miniconda.html.

Create and activate a conda environment:

When using InSituPy with SpatialData, python version 3.13 is mandatory. Otherwise all python version >=3.12 should work.

conda create --name insitupy python=3.13
conda activate insitupy

Install from PyPi:

pip install insitupy-spatial

This base installation includes napari and related visualization dependencies.

InSituPy currently requires zarr>=3.0.0 and targets the zarr v3 format. Legacy zarr v2 workflows are only partially supported and not tested.

Optional: install with SpatialData support (spatialdata>=0.8.0,<0.9.0):

pip install insitupy-spatial[spatialdata]

To ensure that the InSituPy package is available as a kernel in Jupyter notebooks within your conda environment, you can follow the instructions here.

For alternative installation strategies see the documentation.

Features

• Data storage: Store data on both the single sample level and the multi-sample level using the InSituData and InSituExperiment objects.
• Data Preprocessing: InSituPy provides functions for normalizing, filtering, and transforming raw in situ transcriptomics data.
• Interactive Visualization: Create interactive plots using napari to easily explore spatial gene expression patterns.
• Annotation: Annotate Xenium In Situ data in the napari viewer or import annotations from external tools like QuPath.
• Multi-sample analysis: Perform analysis on an experiment-level, i.e. with multiple samples at once.

QuPath

We try to develop InSituPy alongside the Bioimage Analysis tool QuPath. QuPath has great functionalities to visualize whole slide image data, add annotations, generate segmentations or analyze signal intensities. Scripts to simplify the connection between QuPath and InSituPy, we collect here. This includes:

• Export of annotations as GEOJSON from QuPath
• Export of images as OME-TIFF from QuPath
• Collected export of data from a multiplexed IF image to be imported into InSituPy. Import can be performed using either read_qupath or read_qupath_project. For cell and nucleus segmentation of multiplexed IF images we recommend using Instanseg.

Contributing

Contributions are welcome! If you find any issues or have suggestions for new features, please open an issue, submit a pull request or contact us via our zulip chat.

Before opening a pull request, please read the Contributing Guide and, if you used an AI assistant, the AI Policy. The repo also ships an in-repo AI dev-workflow (/review, /plan, /implement) usable across common AI coding agents.

Citation

If you use InSituPy in your work, please cite the preprint as follows:

InSituPy – A Framework for Histology-Guided, Multi-Sample Analysis of Single-Cell Spatial Transcriptomics Data.
Wirth, Johannes, Anna Chernysheva, Birthe Lemke, Isabel Giray, Aitana Egea Lavandera, and Katja Steiger.
bioRxiv, March 12, 2025. https://doi.org/10.1101/2025.03.07.641860.

License

InSituPy is licensed under the BSD-3-Clause.

InSituPy is developed and maintained by Johannes Wirth and Anna Chernysheva. Feedback is highly appreciated and hopefully InSituPy helps you with your analysis of spatial transcriptomics data. The package is thought to be a starting point to simplify the analysis of in situ sequencing data in Python and it would be exciting to integrate functionalities for larger and more comprehensive data structures. Currently, the framework focuses on the analysis of Xenium In Situ data but it is planned to integrate more methodologies and any support on this is highly welcomed.