A Python toolkit for subcellular analysis of spatial transcriptomics data
☆89Nov 16, 2025Updated 8 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☆87Jul 2, 2026Updated 2 weeks ago
- Build contrasts for models defined with formulaic☆13Jul 13, 2026Updated last week
- An open and interoperable data framework for spatial omics data☆382Updated this week
- Automatically annotate cell types, consistently across samples.☆25Jul 13, 2026Updated last week
- A performant scientific image visualization system.☆36Updated 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.
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆109Jul 13, 2026Updated last week
- Sub-cellular spatial transcriptomics Cell Segmentation☆71Oct 1, 2023Updated 2 years ago
- Fast array utilities☆15Updated this week
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆102Dec 11, 2023Updated 2 years ago
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 2 years ago
- ☆31Updated this week
- ☆47Jun 1, 2026Updated last month
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆56Nov 13, 2025Updated 8 months ago
- A multi-dimensional spatial image data structure for scientific Python.☆44Aug 8, 2025Updated 11 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Bayesian Segmentation of Spatial Transcriptomics Data☆208Jun 26, 2026Updated 3 weeks ago
- Python API and Jupyter widget for Vitessce☆67Jun 10, 2026Updated last month
- ☆18May 15, 2026Updated 2 months ago
- ☆74May 28, 2025Updated last year
- CAST package☆44Oct 26, 2024Updated last year
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆16Feb 27, 2026Updated 4 months ago
- ☆16Apr 7, 2026Updated 3 months ago
- Spatial Single Cell Analysis in Python☆584Jul 13, 2026Updated last week
- ☆13Aug 9, 2022Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆288Updated this week
- ☆29Apr 26, 2024Updated 2 years ago
- Single-cell spatial omics analysis that makes you happy!☆70Jul 13, 2026Updated last week
- FA2021 Bootcamp course website for the incoming cohort of the Bioinformatics & Systems Biology Ph.D. program☆20Sep 16, 2021Updated 4 years ago
- Minimum Information about Tissue Imaging☆21Oct 18, 2023Updated 2 years ago
- ☆17May 21, 2026Updated 2 months ago
- ☆100Jul 2, 2026Updated 2 weeks ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆143Jul 8, 2026Updated last week
- Utilities for large scale distributed single cell data processing☆24Jan 20, 2026Updated 6 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated last year
- Single-cell differential expression☆19Apr 23, 2026Updated 2 months ago
- Genomic Features in Python from BioConductor's AnnotationHub☆23Jul 13, 2026Updated last week
- Linking napari layers with Matplotlib plots☆45Jul 1, 2026Updated 2 weeks ago
- Interoperability between SpatialData and the Xenium Explorer☆26Jul 31, 2024Updated last year
- Conditional Autoencoders for Multiplexed Pixel Analysis☆19Nov 25, 2022Updated 3 years ago
- A probabilistic factor model for spatial transcriptomics data with subcellular resolution☆25May 3, 2023Updated 3 years ago