Single Cell Spatial Transcriptomics Tools

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Table of Contents

• Quality Control
• Segmentation
• Cell typing
• Cell Deconvolution
• Domain identification
• Genes imputation
• Spatially variable genes
• Cell-cell communications
• Dimension reduction
• Multimodal integration
• Foundation models
• Other tools
• Contributors

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🔍 Quality Control

Tools for quality control and artifact detection in spatial transcriptomics data.

Name	Released	Documentation	Links
SpatialQC	08/2024
MerQuaCo	03/2025

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🔬 Segmentation

Tools for cell segmentation and boundary detection in spatial transcriptomics data.

Name	Released	Documentation	Links
sopa	06/2024
CellSAM	02/2025	N/A
Segger	03/2025	N/A
BOMS	06/2025	N/A
Bering	07/2025

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🏷️ Cell typing

Tools for annotating and classifying cell types in spatial data.

Name	Released	Documentation	Links
TANGRAM	10/2021
cell2location	01/2022
cellTypist	05/2022
CellAnnotator	03/2024
Nico	12/2024

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🧩 Cell Deconvolution

Tools for deconvolving cell type composition from spatial transcriptomics data.

Name	Released	Documentation	Links
SpatialcoGCN	05/2024	N/A
STdGCN	08/2024	N/A
SDePER	10/2024
CLPLS	02/2025	N/A
NODE	02/2025	N/A
DECLUST	07/2025	N/A

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🗺️ Domain identification

Tools for identifying and clustering spatial domains and tissue structures.

Name	Released	Documentation	Links
SpaGCN	10/2021	N/A
STAGATE	04/2022
CCST	06/2022	N/A
SpaceFlow	07/2022	N/A
DeepST	12/2022	N/A
GraphST	03/2023
SPACEL	11/2023	N/A
CellCharter	12/2023
Banksy	02/2024	N/A
SCGP	08/2024	N/A
SR-DGN	11/2024	N/A
MAEST	03/2025	N/A
SpaGT	04/2025

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🧬 Genes imputation

Tools for imputing missing gene expression values in spatial datasets.

Name	Released	Documentation	Links
SpaOTsc	04/2020	N/A
SpaGE	09/2020	N/A
novoSpaRc	08/2021	N/A
TANGRAM	10/2021
stMCDI	03/2024	N/A
stDiff	04/2024	N/A
SpotGF	10/2024	N/A
stImpute	10/2024	N/A
stGRL	07/2025	N/A

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📊 Spatially variable genes

Tools for identifying genes with spatial expression patterns.

Name	Released	Documentation	Links
SpatialDE	03/2018	N/A
Hotspot	05/2021
SOMDE	12/2021	N/A
SINFONIA	02/2023
Maxspin	06/2023	N/A
SC2Spa	08/2023	N/A

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💬 Cell-cell communications

Tools for analyzing intercellular communication and signaling pathways.

Name	Released	Documentation	Links
CellphoneDB	11/2018
NATMI	10/2020	N/A
Tensor cell2cell	06/2022
NCEM	10/2022
COMMOT	01/2023
Holonet	11/2023
stLearn	11/2023
FlowSig	08/2024	N/A
DeepTalk	08/2024
LIANA+	09/2024
SpaCCC	12/2024	N/A
SpaCcLink	02/2025	N/A
scNiche	02/2025	N/A
NicheCompass	03/2025

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📐 Dimension reduction

Tools for reducing dimensionality while preserving spatial information.

Name	Released	Documentation	Links
SpatialPCA	11/2022
STAMP	10/2024
GraphPCA	11/2024	N/A

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🔗 Multimodal integration

Tools for integrating multiple data modalities and spatial omics datasets.

Name	Released	Documentation	Links
SpaGCN	10/2021	N/A
STACI	12/2022	N/A
STAligner	10/2023
SpatialScope	11/2023
Starfysh	03/2024	N/A
SpatiaGlue	06/2024
DeepTalk	08/2024
METI	08/2024	N/A
CAST	09/2024
STANDS	09/2024
Monae	10/2024	N/A
ISS-Patcher	11/2024
MISO	01/2025	N/A
INSTINCT	02/2025	N/A
SMODEL	06/2025	N/A

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🤖 Foundation models

Large-scale pre-trained models for spatial transcriptomics analysis.

Name	Released	Documentation	Links
Nicheformer	04/2024	N/A
scGPT-spatial	02/2025	N/A
SpatialAgent	04/2025	N/A
OmiCLIP	05/2025	N/A
stFormer	08/2025	N/A

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🛠️ Other tools

Additional specialized tools for spatial transcriptomics analysis.

Name	Released	Purpose	Documentation	Links
SpaCell	04/2020	Predict disease cells	N/A
scArches	08/2021	Mapping sc to reference atlas by transfer learning
eggplant	11/2021	Common Coordinate Framework
scvi-tools	02/2022	probabilistic analysis of single cell
PathML	02/2022	computational pathology
CytoCommunity	01/2024	identification of tissue cellular neighborhoods	N/A
scCube	06/2024	simulation of spatially transcriptomics data	N/A
Bento	04/2024	subcellular analysis
SANTO	07/2024	coarse-to-fine alignment and stitching	N/A
SpaGFT	08/2024	Graph Fourier transform for spatial omics
InSTAnT	09/2024	Intracellular patterns of co-localisation	N/A
MuSpan	02/2025	Multiscale analysis
DeepSpot	02/2025	Spatial transcriptomics Prediction from H&E images	N/A
InSituPy	03/2025	histology-guided, multi-sample analysis of single-cell spatial transcriptomics
MESA	04/2025	ecological inspired spatial analysis

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✨ Contributors

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