Single-cell spatial omics analysis that makes you happy!
☆69Jun 29, 2026Updated this week
Alternatives and similar repositories for harpy
Users that are interested in harpy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Interactive visualization of spatial omics data☆87Updated this week
- Static plotting for spatialdata☆82Jun 24, 2026Updated last week
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Jun 26, 2026Updated last week
- Automatically annotate cell types, consistently across samples.☆24Jun 22, 2026Updated last week
- ☆99Jun 8, 2026Updated 3 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆67Jun 15, 2026Updated 2 weeks ago
- Build contrasts for models defined with formulaic☆13Updated this week
- Python API and Jupyter widget for Vitessce☆67Jun 10, 2026Updated 3 weeks ago
- Jupyter notebook based multiplex image processing pipeline.☆10Jun 23, 2026Updated last week
- Efficient data structures and IO for whole slide image analysis☆27Jun 20, 2026Updated 2 weeks ago
- ☆226Feb 4, 2026Updated 5 months ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆109Jun 22, 2026Updated last week
- A minimal Python package for reading, writing and validating OME-Zarr (meta)data☆39Jun 25, 2026Updated last week
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆44Jun 11, 2026Updated 3 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Probabilistic cell segmentation for in situ spatial transcriptomics☆180Jun 26, 2026Updated last week
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆136Jun 26, 2026Updated last week
- ☆74May 28, 2025Updated last year
- An open and interoperable data framework for spatial omics data☆381Jun 24, 2026Updated last week
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆378Jun 26, 2026Updated last week
- Registry for scverse ecosystem packages☆37Jun 22, 2026Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆87Nov 16, 2025Updated 7 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆89May 25, 2026Updated last month
- Simple scVI implementation☆13May 25, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆35Jun 23, 2026Updated last week
- Package for the analysis of Transcripts outside segmented cells in ST data☆30Jun 22, 2026Updated last week
- A relabeling tool for tiled segmentation with Dask☆18Sep 24, 2024Updated last year
- ☆34Oct 10, 2025Updated 8 months ago
- A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.☆18Jun 22, 2026Updated last week
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆56Nov 13, 2025Updated 7 months ago
- ☆15Apr 7, 2026Updated 2 months ago
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆16Feb 27, 2026Updated 4 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆283Jun 24, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Spatial omics analysis and visualization library☆25Updated this week
- Integrated pipeline for multiplexed image analysis☆107Jan 7, 2026Updated 5 months ago
- Read, create and write cutting data for the Leica LMD6 & LMD7 microscope. Build reproducible workflows to calibrate, import SVG files and…☆15Jun 11, 2026Updated 3 weeks ago
- ☆19May 12, 2026Updated last month
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆19Sep 19, 2025Updated 9 months ago
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆25Apr 8, 2025Updated last year
- Vitessce is a visual integration tool for exploration of spatial single-cell experiments.☆255Updated this week