Single-cell spatial omics analysis that makes you happy!
☆61Apr 27, 2026Updated last 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☆85Apr 27, 2026Updated last week
- Automatically annotate cell types, consistently across samples.☆20Updated this week
- Static plotting for spatialdata☆79Apr 27, 2026Updated last week
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Apr 25, 2026Updated last week
- ☆92Apr 27, 2026Updated last week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆65Apr 27, 2026Updated last week
- Efficient data structures and IO for whole slide image analysis☆26Mar 23, 2026Updated last month
- Build contrasts for models defined with formulaic☆12Apr 27, 2026Updated last week
- Python API and Jupyter widget for Vitessce☆66Apr 17, 2026Updated 2 weeks ago
- Jupyter notebook based multiplex image processing pipeline.☆10Apr 16, 2026Updated 2 weeks ago
- ☆219Feb 4, 2026Updated 3 months ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆108Updated this week
- A minimal Python package for reading, writing and validating OME-Zarr (meta)data☆37Apr 23, 2026Updated last week
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆42Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆129Updated this week
- An open and interoperable data framework for spatial omics data☆365Apr 27, 2026Updated last week
- ☆72May 28, 2025Updated 11 months ago
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆360Updated this week
- Registry for scverse ecosystem packages☆36Apr 28, 2026Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆87Nov 16, 2025Updated 5 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆91Mar 16, 2026Updated last month
- Simple scVI implementation☆12Apr 27, 2026Updated last week
- ☆24Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Probabilistic cell segmentation for in situ spatial transcriptomics☆167Apr 28, 2026Updated last week
- Package for the analysis of Transcripts outside segmented cells in ST data☆28Apr 27, 2026Updated last week
- A relabeling tool for tiled segmentation with Dask☆17Sep 24, 2024Updated last year
- ☆34Oct 10, 2025Updated 6 months ago
- A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.☆17Apr 27, 2026Updated last week
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆55Nov 13, 2025Updated 5 months ago
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆16Feb 27, 2026Updated 2 months ago
- ☆15Apr 7, 2026Updated 3 weeks ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆275Apr 23, 2026Updated last week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Spatial omics analysis and visualization library☆25Updated this week
- Integrated pipeline for multiplexed image analysis☆105Jan 7, 2026Updated 3 months ago
- Read, create and write cutting data for the Leica LMD6 & LMD7 microscope. Build reproducible workflows to calibrate, import SVG files and…☆15Jan 17, 2026Updated 3 months ago
- ☆17Feb 24, 2026Updated 2 months ago
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆18Sep 19, 2025Updated 7 months ago
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆25Apr 8, 2025Updated last year
- The complete FlowSOM package known from R, now available in Python!☆29Apr 27, 2026Updated last week