EASI-FISH analysis pipeline for spatial transcriptomics
☆35Nov 18, 2024Updated last year
Alternatives and similar repositories for multifish
Users that are interested in multifish are comparing it to the libraries listed below
Sorting:
- Tools and scripts for EASI-FISH image data analysis☆17Oct 19, 2022Updated 3 years ago
- Tool for precise, interactive, fast and scalable FISH spot detection☆50Feb 4, 2025Updated last year
- Tools for distributed alignment of massive images☆93Updated this week
- Graph-based Decoding for In Situ Sequencing☆10Jul 2, 2020Updated 5 years ago
- Building Gene Sets and Mapping mFISH Data☆16Aug 20, 2025Updated 6 months ago
- ☆13Feb 27, 2024Updated 2 years ago
- Reconstruct big images from overlapping tiled images on a Spark cluster.☆34Oct 17, 2023Updated 2 years ago
- Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery☆14Apr 10, 2025Updated 10 months ago
- Develop custom oligo design pipelines.☆27Updated this week
- Threshold independent detection and localization of diffraction-limited spots.☆38Nov 1, 2022Updated 3 years ago
- Basic example of using OME-Zarr in a Nextflow pipeline☆20Jul 15, 2025Updated 7 months ago
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.☆31May 27, 2025Updated 9 months ago
- ☆53Apr 1, 2021Updated 4 years ago
- nf-tencentcloud is a nextflow plugin designed to add Tencent Cloud Object storage and Tencent Healthcare Omics Platform executor adaptati…☆18Jul 7, 2025Updated 7 months ago
- GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets☆75Feb 15, 2026Updated last week
- Advanced Tool for Labeling And Segmentation☆40Oct 21, 2024Updated last year
- ☆15Apr 2, 2025Updated 10 months ago
- ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration☆164Feb 19, 2026Updated last week
- a free, open-source web app for annotating, training, and evaluating image understanding algorithms☆25Nov 23, 2021Updated 4 years ago
- MERFISH decoding software☆26Aug 16, 2025Updated 6 months ago
- Package for removing motion artifacts from two-channel imaging☆11Aug 29, 2023Updated 2 years ago
- Allen Brain Atlas utilities, parsers and data structures☆11Jun 25, 2017Updated 8 years ago
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆45Jun 13, 2025Updated 8 months ago
- Running compute-intense parts of BigStitcher distributed☆30Feb 10, 2026Updated 2 weeks ago
- Commands and Classes for interfacing between Imaris and Fiji☆13Sep 30, 2024Updated last year
- ☆14Updated this week
- A 3D interactivity toolbox for napari☆37Jul 8, 2025Updated 7 months ago
- ☆29Apr 26, 2024Updated last year
- Problem sets and materials for systems and computational neuroscience course☆16Feb 19, 2026Updated last week
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆35Sep 21, 2021Updated 4 years ago
- A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images☆65Mar 12, 2025Updated 11 months ago
- ☆36Mar 22, 2024Updated last year
- A scalable machine learning pipeline for probe specificity prediction.☆14Jan 23, 2024Updated 2 years ago
- ☆17Jul 8, 2024Updated last year
- Lab for quantitative bioimage analysis experiments in Python☆19Feb 16, 2026Updated last week
- starfish: unified pipelines for image-based transcriptomics☆244Updated this week
- Bio-Formats image file format to raw format converter☆103Feb 18, 2026Updated last week
- Image reading, metadata management, and image writing for Microscopy images in Python☆114Dec 22, 2025Updated 2 months ago
- ☆15Feb 28, 2022Updated 3 years ago