Wiki

Topics · Data · Molecular data

Spatial omics

Work that measures or analyses molecules while keeping the position of each cell or spot in the tissue, such as spatial transcriptomics or proteomics. Not for imaging without molecular measurements.

In Data › Molecular data62 works2 people20 toolsSingle-cell and spatial atlases

The map of publications with the 62 works under Spatial omics drawn large in the colour of their first topic's group.62 of 743 works marked · data synced 7 Nov 2026

People2

  • Fabian Theis

    Principal investigator

    Single-cell genomics · Bulk omics and genetics · Perturbation responses

AlumniIlan Gold

Publications62

In the publication list
  1. Deep learning and generative models
  2. Deep learning and generative models
  3. Immunity and inflammation
  4. Spatial omics
  5. Spatial omics
  6. Deep learning and generative models
  7. Deep learning and generative models
  8. Spatial omics
  9. Cell atlases
  10. Data integration
  11. Spatial omics
  12. Deep learning and generative models
  13. Single-cell genomics
  14. Spatial omics
  15. Open-source software
  16. Cell atlases
  17. Data integration
  18. Deep learning and generative models
  19. Spatial omics
  20. Deep learning and generative models
  21. Spatial omics
  22. Deep learning and generative models
  23. Gene regulation
  24. Spatial omics
  25. Spatial omics
  26. Benchmarks and best practices
  27. Cell atlases
  28. Deep learning and generative models
  29. Deep learning and generative models
  30. Benchmarks and best practices
  31. Metabolism and diabetes
  32. Spatial omics
  33. Single-cell genomics
  34. Brain and mental health
  35. Spatial omics
  36. Open-source software
  37. Gene regulation
  38. Deep learning and generative models
  39. Single-cell genomics
  40. Spatial omics
  41. Data integration
  42. Brain and mental health
  43. Spatial omics
  44. Deep learning and generative models
  45. Cell fate and dynamics
  46. Spatial omics
  47. Single-cell genomics
  48. Spatial omics
  49. Deep learning and generative models
  50. Single-cell genomics
  51. Immunity and inflammation
  52. Spatial omics
  53. Deep learning and generative models
  54. Spatial omics
  55. Data integration
  56. Spatial omics
  57. Open-source software
  58. Spatial omics
  59. Cell atlases
  60. Immunity and inflammation
  61. Spatial omics
  62. Cell atlases

Software20

  • Squidpy

    Spatial Single Cell Analysis in Python

    612v1.8.49 d agoPython

  • SpatialData

    An open and interoperable data framework for spatial omics data

    407v0.8.04 mo agoPython

  • moscot

    Multi-omic single-cell optimal transport tools.

    219v0.5.22 mo agoPython

  • nicheformer

    Repository for Nicheformer: a foundation model for single-cell and spatial omics

    179Jupyter Notebook

  • spapros

    Python package for Probe set selection for targeted spatial transcriptomics.

    510.1.612 mo agoPython

  • graphcompass

    GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems

    39Jupyter Notebook

  • troutpy

    Package for the analysis of Transcripts outside segmented cells in ST data

    32v0.2.026 d agoJupyter Notebook

  • campa

    Conditional Autoencoders for Multiplexed Pixel Analysis

    19v1.1.04 y agoJupyter Notebook

  • interscale

    InterScale: multi-scale cellular interaction analysis model for spatial transcriptomics

    14v0.2.06 mo agoPython

  • deconvATAC

    Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data

    6Jupyter Notebook

  • spatial_atlas_ssl

    Self-supervised learning for mask inpainting on large spatial atlasses such as the BICCN 2.0 data.

    5Jupyter Notebook

  • txsim

    5v0.1.22 y agoPython

  • sprotmetrics

    Quality metrics for imaging-based spatial proteomics: segmentation, signal-to-background, normalization, marker distribution and technical-covariate diagnostics.

    2v0.1.019 d agoPython