Toolbox for the analysis of smFISH images.
☆78Oct 31, 2023Updated 2 years ago
Alternatives and similar repositories for big-fish
Users that are interested in big-fish are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Notebooks to illustrate how BigFISH is working.☆12Sep 5, 2022Updated 3 years ago
- Tool for precise, interactive, fast and scalable FISH spot detection☆54Feb 4, 2025Updated last year
- Repository to automatically process Fluorescence In Situ Hybridization (FISH) images using Cellpose and BIG-FISH (FISH-quant v2).☆17Dec 16, 2024Updated last year
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 4 years ago
- Deep learning based spot detection for FISH images.☆35Jan 7, 2026Updated 6 months ago
- 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.
- Guides and code for 3D nuclear instance segmentation☆23Dec 2, 2025Updated 7 months ago
- A JupyterBook site for napari workshop materials☆10Jul 11, 2022Updated 4 years ago
- ☆21Updated this week
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Jun 13, 2025Updated last year
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆38Jul 7, 2026Updated 3 weeks ago
- Accurate and efficient spot detection for microscopy data☆138Jun 8, 2026Updated last month
- ☆29Apr 26, 2024Updated 2 years ago
- A napari plugin for stitching large multi-positioning datasets in 2/3D+t using multiview-stitcher☆19Updated this week
- Training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material will develop betwee…☆39Jul 9, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets☆31May 28, 2026Updated 2 months ago
- Fast writing of numpy 3d-arrays into HDF5 Fiji/BigDataViewer files.☆34Aug 22, 2024Updated last year
- Kaibu -- a progressive web app for visualizing and annotating multi-dimensional images.☆35Apr 4, 2025Updated last year
- ☆18Mar 31, 2024Updated 2 years ago
- Process images using SimpleITK in napari☆23May 1, 2025Updated last year
- comseg☆24Feb 6, 2025Updated last year
- An automated point-set based registration algorithm for correlative light and electron microscopy (CLEM)☆22Mar 12, 2026Updated 4 months ago
- Deconvolution of widefield microscopy images and generation of point spread functions☆65Jul 3, 2026Updated 3 weeks ago
- Block-wise operations for large nD volumes☆45Updated this week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆23Mar 26, 2021Updated 5 years ago
- BIRDS plug-in on Fiji and attached jar package☆22Oct 7, 2021Updated 4 years ago
- Teaching materials and outline for the Pasteur Bioimage Analysis vour☆17Jun 2, 2025Updated last year
- ImageJ macros and scripts written at the imaging facility MRI☆43Updated this week
- ☆17May 21, 2026Updated 2 months ago
- Spotiflow plugin for napari☆19May 19, 2026Updated 2 months ago
- ☆11May 6, 2024Updated 2 years ago
- MorphoFeatures code and data☆23May 11, 2026Updated 2 months ago
- starfish: unified pipelines for image-based transcriptomics☆249Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A probabilistic cell typing algorithm for spatial transcriptomics.☆26Jun 24, 2026Updated last month
- ImJoy Plugin Engine for running Python plugins locally or remotely from ImJoy.io☆18Aug 16, 2022Updated 3 years ago
- WebGL-based viewer for spatially-resolved transcriptomics data☆28Jan 6, 2023Updated 3 years ago
- Automated Cell Toolkit☆24Oct 15, 2025Updated 9 months ago
- ☆15May 22, 2025Updated last year
- FISH Iterative Cell Typing☆11Mar 24, 2024Updated 2 years ago
- Repo for the CZI Imaging Team's napari plugin Alfa Cohort collaboration☆11May 14, 2021Updated 5 years ago