Single-cell spatial omics analysis that makes you happy.

Documentation · Quick Start · Tutorials · spatiato · harpy-vitessce

💫 If you find Harpy useful, please give us a ⭐! It helps others discover the project and supports continued development.

Why Harpy?

Harpy is a spatial omics analysis library for spatial transcriptomics and proteomics, and part of the scverse ecosystem. It bridges SpatialData and downstream analysis tools such as AnnData, Scanpy, and Squidpy. It provides scalable, image- and geometry-aware computation to transform raw spatial data into analysis-ready representations, with a strong emphasis on interoperability and large-scale workflows.

In practice, Harpy offers fast, out-of-core image preprocessing, tiled segmentation, along with efficient aggregation workflows to generate AnnData tables and compute per-cell features from images, segmentation masks, and transcript coordinates. It also supports deep feature extraction, pixel- and cell-level clustering, and the construction of single-cell representations from highly multiplexed images.

• Multi-platform support for spatial transcriptomics and proteomics data.
• Interoperable outputs built on SpatialData.
• SpatialData and AnnData ergonomics: read single tables and write only the components that changed (obs, obsm, uns, …) to a backed Zarr store with harpy.tb.io; add images, labels, shapes and points with harpy.im, harpy.sh and harpy.pt.
• Scales to (very) large images: tiled workflows with Dask; optional GPU acceleration with CuPy and PyTorch.
• Scalable computational building blocks for segmentation, feature extraction, clustering, and spatial analysis.

Development and support

Harpy is actively developed and maintained by the Saeys Lab and VIB Spatial Catalyst, part of VIB Technologies. VIB funds a dedicated development team, so Harpy gets long-term maintenance and continued development.

Installation

pip install harpy-analysis

Optional extras:

Extra	Installs
[extra]	Segmentation (cellpose, instanseg-torch), OpenCV (opencv-python-headless), Vitessce (harpy-vitessce) and notebook tools (marimo, ipywidgets, tqdm, …)
[spatiato]	spatiato, the spatial omics interface for napari

pip install "harpy-analysis[extra]"

For the developer setup and more details, see the installation guide.

Quickstart

See the short, runnable guide.

Ecosystem

• spatiato: a spatial omics interface for napari, built on SpatialData and Harpy, for interactive exploration and analysis of SpatialData stores.
• harpy-vitessce: interactive visualization of Harpy outputs with Vitessce.
• Spatial multi-omics training: course notebooks on SpatialData objects, targeted transcriptomics and spatial proteomics with Harpy and spatiato.

Computational benchmark

Explore the benchmark performance of Harpy on a large MACSima tonsil proteomics dataset. 👉 Results

Contributing

See the contribution guide for info on how to contribute to Harpy.

Citation

If you use Harpy in your work, please cite:

Benjamin Rombaut, Arne Defauw, Frank Vernaillen, Julien Mortier, Evelien Van Hamme, Sofie Van Gassen, Ruth Seurinck, Yvan Saeys. Scalable analysis of whole slide spatial proteomics with Harpy. Bioinformatics (2026), btag122. https://doi.org/10.1093/bioinformatics/btag122

If you use Harpy for spatial transcriptomics analysis, please cite:

Lotte Pollaris, Bavo Vanneste, Benjamin Rombaut, Arne Defauw, Frank Vernaillen, Julien Mortier, Wout Vanhenden, Liesbet Martens, Tinne Thone, Jean-Francois Hastir, Anna Bujko, Wouter Saelens, Jean-Christophe Marine, Hilde Nelissen, Evelien Van Hamme, Ruth Seurinck, Charlotte L. Scott, Martin Guilliams, Yvan Saeys. SPArrOW: a flexible, interactive and scalable pipeline for spatial transcriptomics analysis. https://doi.org/10.1101/2024.07.04.601829

BibTeX

@article{rombaut2026harpy,
  title   = {Scalable analysis of whole slide spatial proteomics with Harpy},
  author  = {Rombaut, Benjamin and Defauw, Arne and Vernaillen, Frank and Mortier, Julien and Van Hamme, Evelien and Van Gassen, Sofie and Seurinck, Ruth and Saeys, Yvan},
  journal = {Bioinformatics},
  volume  = {42},
  number  = {3},
  pages   = {btag122},
  year    = {2026},
  doi     = {10.1093/bioinformatics/btag122}
}

@article{pollaris2024sparrow,
  title   = {SPArrOW: a flexible, interactive and scalable pipeline for spatial transcriptomics analysis},
  author  = {Pollaris, Lotte and Vanneste, Bavo and Rombaut, Benjamin and Defauw, Arne and Vernaillen, Frank and Mortier, Julien and Vanhenden, Wout and Martens, Liesbet and Thon{\'e}, Tinne and Hastir, Jean-Francois and Bujko, Anna and Saelens, Wouter and Marine, Jean-Christophe and Nelissen, Hilde and Van Hamme, Evelien and Seurinck, Ruth and Scott, Charlotte L. and Guilliams, Martin and Saeys, Yvan},
  journal = {bioRxiv},
  year    = {2024},
  doi     = {10.1101/2024.07.04.601829}
}

License

Harpy is licensed under the BSD 3-Clause License.

Issues

If you encounter any problems, please file an issue along with a detailed description.