---
title: "Spatial Transcriptomics Data I/O - Air Market"
description: "Your spatial transcriptomics data came off one platform and your analysis expects another shape. This loads runs from Visium, Xenium, MERFISH, Slide-seq and other platforms, and converts between the…"
canonical: "https://airmarket.ai/app/spatial-transcriptomics-spatial-data-io"
---

[Air Market](/) / [Data & Analytics](/category/data) / Spatial Transcriptomics Data I/O

Skill by [PharMolix](/@pharmolix)

# Spatial Transcriptomics Data I/O

Get spatial data off the instrument and into your analysis

## What this does

Your spatial transcriptomics data came off one platform and your analysis expects another shape. This loads runs from Visium, Xenium, MERFISH, Slide-seq and other platforms, and converts between the two data formats. Reach for it at the point where getting the data in is the obstacle.

### Top 3 things it does for you

- Load Visium data from Space Ranger output
- Load single-cell resolution Xenium data
- Load MERFISH, CosMx or Slide-seq runs

## Information

**Spatial Transcriptomics Data I/O at a glance**

|  |  |
| --- | --- |
| Kind | Skill |
| Publisher | [PharMolix](/@pharmolix) |
| Category | [Data & Analytics](/category/data) |
| Works with | Agent Skills - an open standard supported by 40+ agents |
| Size | 11 KB |
| Licence | MIT |
| Repository | [PharMolix/OpenBioMed](https://github.com/PharMolix/OpenBioMed/tree/0eea7482ce1718ff04a70dec51ec73bb93130036/skills/spatial-transcriptomics-spatial-data-io) |
| GitHub stars | 1,103 (as of Nov 2026) |

## Security report

**Verified.** AIR scanned this exact version of Spatial Transcriptomics Data I/O and flagged nothing. AIR's verdict: **safe**.

**What Spatial Transcriptomics Data I/O's check was run against**

|  |  |
| --- | --- |
| Commit | 0eea7482ce1718ff04a70dec51ec73bb93130036 |
| Content hash | 4faaac64c790df715b6eba5bf755b683449f2838dcaf2cbd6ce05e6557f75e68 |
| Files read | [Browse the files at this exact commit](https://github.com/PharMolix/OpenBioMed/blob/0eea7482ce1718ff04a70dec51ec73bb93130036/skills/spatial-transcriptomics-spatial-data-io/SKILL.md) |

A scan is named by the exact content it read, not by a version number. A different version is a different artifact, and nothing here applies to a version AIR has not scanned.

[Read the full security report for Spatial Transcriptomics Data I/O](/security/spatial-transcriptomics-spatial-data-io)

## About Spatial Transcriptomics Data I/O

This skill loads spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq and other platforms, using Squidpy and SpatialData.

It covers Visium data from Space Ranger output, Xenium single-cell resolution data, and MERFISH, CosMx and other spatial platforms, and converts between SpatialData and AnnData formats.

## What's inside

- SKILL.md - instructions

## Questions

### Is Spatial Transcriptomics Data I/O safe to install?

AIR scanned this exact version of Spatial Transcriptomics Data I/O and flagged nothing. AIR's verdict: safe. The verdict is named by the content that was read, at commit 0eea7482ce17, so it cannot drift onto a version nobody scanned. The full report is at https://airmarket.ai/security/spatial-transcriptomics-spatial-data-io.

### How do I install Spatial Transcriptomics Data I/O?

Open https://airmarket.ai/app/spatial-transcriptomics-spatial-data-io on Air Market and use the install action: Air Market hands Claude a prompt naming this exact skill, and Claude sets it up. Source, pinned to the exact commit this listing describes: https://github.com/PharMolix/OpenBioMed/tree/0eea7482ce1718ff04a70dec51ec73bb93130036/skills/spatial-transcriptomics-spatial-data-io. Install from that link, not the branch.

## Related on Air Market

- [More Data & Analytics listings](/category/data)
- [Everything by PharMolix](/@pharmolix)

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Canonical URL: <https://airmarket.ai/app/spatial-transcriptomics-spatial-data-io>