starfish: unified pipelines for image-based transcriptomics
☆250Aug 6, 2026Updated 3 weeks ago
Alternatives and similar repositories for starfish
Users that are interested in starfish are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Software for exploration of gene expression data from single-cell RNA sequencing.☆28Jun 20, 2019Updated 7 years ago
- Analysis of smFISH data☆12Aug 27, 2018Updated 8 years ago
- An interactive explorer for single-cell transcriptomics data☆785Aug 25, 2026Updated last week
- Deep Learning Library for Spot Detection☆24Jun 4, 2026Updated 2 months ago
- ☆31Apr 26, 2024Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- WebGL-based viewer for spatially-resolved transcriptomics data☆28Jan 6, 2023Updated 3 years ago
- Bayesian Segmentation of Spatial Transcriptomics Data☆212Jul 31, 2026Updated last month
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆37Sep 21, 2021Updated 4 years ago
- Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets☆107Aug 2, 2023Updated 3 years ago
- Spatial Single Cell Analysis in Python☆595Updated this week
- Threshold independent detection and localization of diffraction-limited spots.☆39Apr 8, 2026Updated 4 months ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆89Nov 16, 2025Updated 9 months ago
- ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration☆181Aug 7, 2026Updated 3 weeks ago
- Microscopy Image Cytometry Toolkit☆117Jul 15, 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.
- COMET Single-Cell Marker Detection tool☆33Jun 21, 2022Updated 4 years ago
- Spatial omics analysis toolbox☆388Updated this week
- A scalable machine learning pipeline for probe specificity prediction.☆14Aug 14, 2026Updated 2 weeks ago
- Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…☆70Dec 3, 2025Updated 9 months ago
- A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.☆85Jul 24, 2026Updated last month
- Tool for precise, interactive, fast and scalable FISH spot detection☆54Feb 4, 2025Updated last year
- Test genes for Spatial Variation☆189May 7, 2024Updated 2 years ago
- multimodal whole slide image registration in a graph structure☆103Jul 4, 2024Updated 2 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆36Apr 15, 2026Updated 4 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.
- napari: a fast, interactive, multi-dimensional image viewer for python☆2,751Updated this week
- Software for processing and analyzing STARmap experiments.☆39Aug 27, 2019Updated 7 years ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆462Aug 17, 2026Updated 2 weeks ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆481Jan 22, 2026Updated 7 months ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,551Updated this week
- Integrated pipeline for multiplexed image analysis☆108Aug 20, 2026Updated last week
- Examples using Clustergrammer2 to explore high-dimensional datasets.☆40Aug 24, 2020Updated 6 years ago
- Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python☆221Dec 1, 2025Updated 9 months ago
- CellRank: dynamics from multi-view single-cell data☆456Updated this week
- 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.
- Detect doublets in single-cell RNA-seq data☆85Jul 3, 2019Updated 7 years ago
- Spatial analysis toolkit for single cell multiplexed tissue data☆30Sep 2, 2024Updated 2 years ago
- MERFISH decoding software☆29Aug 16, 2025Updated last year
- Vitessce is a visual integration tool for exploration of spatial single-cell experiments.☆264Updated this week
- ☆27Oct 12, 2024Updated last year
- Spatial alignment of single cell transcriptomic data.☆371Jul 1, 2025Updated last year
- Pydantic models for OME-NGFF☆24Sep 14, 2025Updated 11 months ago