From 856262e7e311199802e4e82db797248561972dab Mon Sep 17 00:00:00 2001 From: Kalin Nonchev Date: Tue, 14 Jul 2026 14:50:37 +0200 Subject: [PATCH 1/4] Add DeepSpot method Co-authored-by: Cursor --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 0eb6f73..bc5c705 100644 --- a/README.md +++ b/README.md @@ -53,6 +53,7 @@ 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|[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)| From 6180e8275abbe9c18fe320d085237f2d29a33ab3 Mon Sep 17 00:00:00 2001 From: Kalin Nonchev Date: Tue, 14 Jul 2026 14:50:42 +0200 Subject: [PATCH 2/4] Add DeepSpot2Cell method Co-authored-by: Cursor --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 0eb6f73..6dc5969 100644 --- a/README.md +++ b/README.md @@ -53,6 +53,7 @@ Following subsection will be subsequently divided by argument while collecting t ### Spatial Transcriptomics Methods & Tools |Year|Title|Language|Description|Reference| |:-:|:--|:-:|:--|:--| +|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)| |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)| From c54faabad67091271c1fe0aea3d283651f071231 Mon Sep 17 00:00:00 2001 From: Kalin Nonchev Date: Tue, 14 Jul 2026 14:50:47 +0200 Subject: [PATCH 3/4] Add DeepSpot-M method Co-authored-by: Cursor --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 0eb6f73..74f1d45 100644 --- a/README.md +++ b/README.md @@ -53,6 +53,7 @@ Following subsection will be subsequently divided by argument while collecting t ### Spatial Transcriptomics Methods & Tools |Year|Title|Language|Description|Reference| |:-:|:--|:-:|:--|:--| +|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)| |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)| From 00658ad82474b5934230af3512df2a262e11a827 Mon Sep 17 00:00:00 2001 From: Kalin Nonchev Date: Tue, 14 Jul 2026 14:50:52 +0200 Subject: [PATCH 4/4] Add AESTETIK method Co-authored-by: Cursor --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 0eb6f73..ba5ee24 100644 --- a/README.md +++ b/README.md @@ -53,6 +53,7 @@ Following subsection will be subsequently divided by argument while collecting t ### Spatial Transcriptomics Methods & Tools |Year|Title|Language|Description|Reference| |:-:|:--|:-:|:--|:--| +|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)|