starfish: unified pipelines for image-based transcriptomics
☆244Mar 19, 2026Updated this week
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 6 years ago
- Analysis of smFISH data☆12Aug 27, 2018Updated 7 years ago
- An interactive explorer for single-cell transcriptomics data☆756Updated this week
- ☆29Apr 26, 2024Updated last year
- Deep Learning Library for Spot Detection☆21Oct 9, 2025Updated 5 months ago
- WebGL-based viewer for spatially-resolved transcriptomics data☆28Jan 6, 2023Updated 3 years ago
- Bayesian Segmentation of Spatial Transcriptomics Data☆202Dec 10, 2024Updated last year
- Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets☆107Aug 2, 2023Updated 2 years ago
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆35Sep 21, 2021Updated 4 years ago
- ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration☆166Feb 19, 2026Updated last month
- Spatial Single Cell Analysis in Python☆555Mar 16, 2026Updated last week
- Test genes for Spatial Variation☆183May 7, 2024Updated last year
- Threshold independent detection and localization of diffraction-limited spots.☆38Nov 1, 2022Updated 3 years ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆88Nov 16, 2025Updated 4 months ago
- Microscopy Image Cytometry Toolkit☆114Jul 15, 2022Updated 3 years ago
- COMET Single-Cell Marker Detection tool☆32Jun 21, 2022Updated 3 years ago
- Spatial omics analysis toolbox☆365Feb 12, 2026Updated last month
- A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.☆83Mar 16, 2026Updated last week
- Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…☆67Dec 3, 2025Updated 3 months ago
- Tool for precise, interactive, fast and scalable FISH spot detection☆50Feb 4, 2025Updated last year
- EASI-FISH analysis pipeline for spatial transcriptomics☆34Nov 18, 2024Updated last year
- multimodal whole slide image registration in a graph structure☆101Jul 4, 2024Updated last year
- napari: a fast, interactive, multi-dimensional image viewer for python☆2,612Updated this week
- Minimum Information about Tissue Imaging☆21Oct 18, 2023Updated 2 years ago
- A scalable machine learning pipeline for probe specificity prediction.☆14Jan 23, 2024Updated 2 years ago
- Software for processing and analyzing STARmap experiments.☆38Aug 27, 2019Updated 6 years ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆108Mar 16, 2026Updated last week
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆422Mar 16, 2026Updated last week
- Single-cell analysis in Python. Scales to >100M cells.☆2,379Updated this week
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆444Jan 22, 2026Updated 2 months ago
- Examples using Clustergrammer2 to explore high-dimensional datasets.☆40Aug 24, 2020Updated 5 years ago
- Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python☆222Dec 1, 2025Updated 3 months ago
- CellRank: dynamics from multi-view single-cell data☆433Mar 9, 2026Updated 2 weeks ago
- Integrated pipeline for multiplexed image analysis☆103Jan 7, 2026Updated 2 months ago
- FISH Iterative Cell Typing☆11Mar 24, 2024Updated last year
- Spatial analysis toolkit for single cell multiplexed tissue data☆30Sep 2, 2024Updated last year
- Detect doublets in single-cell RNA-seq data☆86Jul 3, 2019Updated 6 years ago
- MERFISH decoding software☆26Aug 16, 2025Updated 7 months ago
- Spatial alignment of single cell transcriptomic data.☆359Jul 1, 2025Updated 8 months ago