Empowering spatial transcriptomics research by providing AI agents with a standardized interface to Nextflow pipelines, Viash components, and comprehensive documentation, accelerating discovery in the OpenProblems project.
This repository also configures its own agents. See what SpatialAI_MCP tells them →
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Diagnose a failing Nextflow pipeline run in an OpenProblems benchmark. Use when a nextflow run fails, a process errors out, or the user shares a .nextflow.log / .command.err and asks why it broke.
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Prepare a spatial transcriptomics method for contribution to an OpenProblems benchmark (e.g. taskistpreprocessing). Use when the user wants to submit/contribute a method, open a PR to a task repo, or check submission readiness.
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OpenProblems spatial transcriptomics co-pilot — project rules.
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Validate and inspect spatial transcriptomics data files (SpatialData/zarr/AnnData) before any analysis. Use when the user points at a spatial data file, reports a loading/format error, or asks whether data is suitable for a method.
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Author or modify a Viash component (config.vsh.yaml + script) for an OpenProblems method, especially a taskistpreprocessing stage. Use when the user wants to add/implement a spatial method, scaffold a component, or fix a config.vsh.yaml.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: