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Open-ST is an open-source spatial transcriptomics methodwith efficient whole-transcriptome capture at sub-cellular resolution (0.6 μm) at low cost(<150 Euro library preparation per 12 mm²).

Open-ST requires standard lab equipmentand includes open-source software for seamless data processing and analysis.

• Discuss development onGitHub.
• Read thestep-by-step protocol.
• Install viapip install openst.

We providevarious Open-ST datasets collected by theRajewsky lab @ MDC Berlin, from various tissues/organisms.There, links to raw and processed data are available, as well as step-by-step guides for (pre)processing and downstream analysis.

All the detail to the experimental and computational aspects of our method are available inour website.

We love to have an open approach to documentation. We decided to usemkdocs as our documentation backendto make your life easier. So, feel free to suggest changes by opening adocumentation-related issue!

You can build the documentation locally by following these steps:

1. Clone this repository

   git clone https://github.com/rajewsky-lab/openst

2. Install the dependencies for building the documentation:

   pip install mkdocs-material mkdocs-autorefs mknotebooks

3. Serve mkdocs with the following command:

   mkdocs serve -f openst/mkdocs.yml

Open-ST is an open-source project mostly maintained by theRajewsky lab @ MDC Berlin - so, your involvement is warmly welcome!If you're excited to join us, we recommend the following steps:

• Looking for ideas? See ourVolunteer Project Board to see what we may need help with.
• Found a bug? Contact an admin in the form of anissue.
• Implement your idea following guidelines set by theofficial contributing guide
• Wait for admin approval; approval is iterative, but if accepted will belong to the main repository.

In general, you can always refer to thecontribution guidelines for more details!Currently, onlyadmins will be merging all accepted changes.

Everyone interacting in the Open-ST project's codebases, issue trackers, and discussion forums is expected to follow thePSF Code of Conduct.

The software tools of this project are under the GNU License - see theLICENSE file for details.