A Python toolkit for subcellular analysis of spatial transcriptomics data
☆89Nov 16, 2025Updated 10 months ago
Alternatives and similar repositories for bento-tools
Users that are interested in bento-tools 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☆91Sep 8, 2026Updated last month
- Build contrasts for models defined with formulaic☆13Updated this week
- A performant scientific image visualization system.☆36Aug 5, 2026Updated 2 months ago
- An open and interoperable data framework for spatial omics data☆399Updated this week
- Automatically annotate cell types, consistently across samples.☆30Updated this 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.
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆113Sep 28, 2026Updated last week
- Sub-cellular spatial transcriptomics Cell Segmentation☆71Oct 1, 2023Updated 3 years ago
- Fast array utilities☆15Oct 2, 2026Updated last week
- ☆31Updated this week
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 2 years ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆109Dec 11, 2023Updated 2 years ago
- ☆47Jun 1, 2026Updated 4 months ago
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆58Nov 13, 2025Updated 10 months ago
- A multi-dimensional spatial image data structure for scientific Python.☆45Aug 8, 2025Updated last year
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Bayesian Segmentation of Spatial Transcriptomics Data☆217Oct 2, 2026Updated last week
- Python API and Jupyter widget for Vitessce☆67Sep 22, 2026Updated 2 weeks ago
- ☆20Sep 17, 2026Updated 3 weeks ago
- ☆74May 28, 2025Updated last year
- CAST package☆43Oct 26, 2024Updated last year
- ☆17Sep 27, 2026Updated last week
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆16Feb 27, 2026Updated 7 months ago
- Spatial Single Cell Analysis in Python☆601Updated this week
- ☆13Aug 9, 2022Updated 4 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- ☆31Apr 26, 2024Updated 2 years ago
- Single-cell spatial omics analysis that makes you happy!☆75Updated this week
- FA2021 Bootcamp course website for the incoming cohort of the Bioinformatics & Systems Biology Ph.D. program☆20Sep 16, 2021Updated 5 years ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆295Sep 15, 2026Updated 3 weeks ago
- ☆103Sep 22, 2026Updated 2 weeks ago
- ☆18Sep 30, 2026Updated last week
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆162Sep 18, 2026Updated 3 weeks ago
- Utilities for large scale distributed single cell data processing☆24Jan 20, 2026Updated 8 months ago
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Single-cell differential expression☆19Apr 23, 2026Updated 5 months ago
- Genomic Features in Python from BioConductor's AnnotationHub☆22Sep 28, 2026Updated last week
- Linking napari layers with Matplotlib plots☆47Jul 1, 2026Updated 3 months ago
- Interoperability between SpatialData and the Xenium Explorer☆27Jul 31, 2024Updated 2 years ago
- A probabilistic factor model for spatial transcriptomics data with subcellular resolution☆25May 3, 2023Updated 3 years ago
- Legend made easy for matplotlib☆36Aug 27, 2026Updated last month
- GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems☆39Jul 11, 2025Updated last year