Spatial transcriptomics atlas retrieval

Retrieve measured ST evidence

Describe a biological state, inspect the retrieved tissue locations in spatial context and continue the analysis using their measured evidence cards.

Natural-language queriesSpatial tissue mapsRanked evidence cardsRetrieval-grounded follow-up analysis

01 · Offline construction Measured ST evidence bank

Evidence cards derived from measured atlas spots are embedded in a shared 4,096-dimensional retrieval space.

02 · Online retrieval Natural-language query

The query is embedded with the same model and matched to atlas spots by cosine similarity.

03 · Follow-up analysis Spatially grounded results

Retrieved spots are examined through their tissue coordinates, ranked evidence cards and evidence-grounded dialogue.

Live retrieval

HistAgent Atlas Explorer

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The public demonstration uses a balanced 100,000-spot index; the manuscript analyses use the complete 2.23-million-spot evidence bank. The first search may wait briefly while a ZeroGPU worker starts.