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Add AESTETIK, DeepSpot-M, DeepSpot2Cell, DeepSpot #13

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856262e
Add DeepSpot method
KalinNonchev Jul 14, 2026
6180e82
Add DeepSpot2Cell method
KalinNonchev Jul 14, 2026
c54faab
Add DeepSpot-M method
KalinNonchev Jul 14, 2026
00658ad
Add AESTETIK method
KalinNonchev Jul 14, 2026
9edec89
Merge add-deepspot2cell-entry for combined PR
KalinNonchev Jul 14, 2026
f81916e
Merge add-deepspotm-entry for combined PR
KalinNonchev Jul 14, 2026
f3785ce
Merge add-aestetik-entry for combined PR
KalinNonchev Jul 14, 2026
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -53,6 +53,10 @@ Following subsection will be subsequently divided by argument while collecting t
### Spatial Transcriptomics Methods & Tools
|Year|Title|Language|Description|Reference|
|:-:|:--|:-:|:--|:--|
|2025|[DeepSpot](https://github.com/ratschlab/DeepSpot)|Python|Predicts spatial transcriptomics from H&E images using spatial context and pathology foundation models.|[Nonchev et al. 2025](https://www.medrxiv.org/content/10.1101/2025.02.09.25321567v3)|
|2025|[DeepSpot2Cell](https://github.com/ratschlab/DeepSpot2Cell)|Python|Predicts virtual single-cell spatial transcriptomics from H&E images using spot-level supervision.|[Nonchev et al. 2025](https://openreview.net/forum?id=ofCkwXQKaz)|
|2026|[DeepSpot-M](https://github.com/ratschlab/DeepSpotM)|Python|Multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology.|[Nonchev et al. 2026](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1)|
|2026|[AESTETIK](https://github.com/ratschlab/aestetik)|Python|Convolutional autoencoder for multi-modal spatial transcriptomics representation learning with morphology and topology.|[Nonchev et al. 2026](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btag316/8692433)|
|2025|[ChatSpatial](https://github.com/cafferychen777/ChatSpatial)|Python|MCP server enabling spatial transcriptomics analysis via natural language. Integrates 60+ methods for spatial domains, deconvolution, cell communication, trajectory analysis across Visium, Xenium, MERFISH.|[PyPI](https://pypi.org/project/chatspatial/) / [Docs](https://cafferychen777.github.io/ChatSpatial/)|
|2021|[Giotto](http://spatialgiotto.rc.fas.harvard.edu/)|R|Toolbox for integrative analysis and visualization of spatial expression data|[Dries et al. 2021](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02286-2)|
|2025|[FlashDeconv](https://github.com/cafferychen777/flashdeconv)|Python|High-performance spatial deconvolution using randomized sketching. Processes 1M spots in ~3 min with linear O(N) scaling.|[Yang et al. 2025](https://doi.org/10.64898/2025.12.22.696108)|
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