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Literature Timeline

Interactive timeline of key publications and tool releases in spatial omics. Hover over items for details. Filter by category.

How to Read This Timeline

  • Scroll horizontally to navigate through time (2014-2025)
  • Hover over items for paper details
  • Filter by category using the buttons above
  • Zoom with Ctrl+scroll

The timeline reveals several patterns:

  1. 2014-2016 -- Founding technologies: seqFISH, IMC, MERFISH, and Spatial Transcriptomics established the core modalities (imaging-based vs. sequencing-based).
  2. 2018-2019 -- Platform convergence: Commercial instruments launched (Visium), analysis tools emerged (SpatialDE, StarDist), and new sequencing approaches (Slide-seq, STARmap) expanded the design space.
  3. 2021-2022 -- Methods explosion: The field hit critical mass with tools for every analysis step -- segmentation (Cellpose, Baysor), deconvolution (Cell2location, RCTD, Tangram), spatial domains (BayesSpace, STAGATE), CCC (CellChat, MISTy), and frameworks (Squidpy, Giotto).
  4. 2023-2024 -- Maturation and single-cell resolution: Next-generation platforms (Xenium, Visium HD, CosMx) pushed toward subcellular resolution. Graph neural network methods (GraphST, BANKSY) became dominant for spatial domains. Benchmark studies systematically compared methods.
  5. 2025 -- Foundation models arrive: Nicheformer and Novae represent a shift toward pre-trained models that learn spatial representations across datasets, moving beyond task-specific tools.