A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
☆183Mar 14, 2026Updated 2 months ago
Alternatives and similar repositories for awesome-biological-image-analysis
Users that are interested in awesome-biological-image-analysis are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Imagej toolset to ease hyperstacks visualization and handling☆23Feb 9, 2026Updated 3 months ago
- Gamified image segmentation quality estimation☆19May 1, 2025Updated last year
- ☆15Jul 29, 2022Updated 3 years ago
- A short course exploring several fun and useful notebooks and Napari widgets for deep learning with SAM, Cellpose, Stardist and friends.☆19Dec 9, 2025Updated 5 months ago
- An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code.☆92Mar 24, 2026Updated last month
- 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.
- Lecture materials "Bio-image analysis, biostatistics, programming and machine learning for computational biology" at the Center of Molecu…☆237Sep 11, 2023Updated 2 years ago
- Non-comprehensive list of projects and resources related to open microscopy.☆177Mar 19, 2026Updated 2 months ago
- Single cell Morphology Quality Control (coSMicQC)☆11May 12, 2026Updated last week
- A curated list of awesome cytodata resources☆90Nov 15, 2023Updated 2 years ago
- A napari plugin for stitching large multi-positioning datasets in 2/3D+t using multiview-stitcher☆19Apr 20, 2026Updated 3 weeks ago
- ☆52May 1, 2025Updated last year
- Guides and code for 3D nuclear instance segmentation☆23Dec 2, 2025Updated 5 months ago
- Awesome list of computational biology.☆134Updated this week
- An introduction to bioimage analysis - http://bioimagebook.github.io☆76Feb 5, 2026Updated 3 months ago
- 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.
- A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)☆20May 1, 2026Updated 2 weeks ago
- A list of web-based interactive biological data visualizations.☆228Apr 2, 2024Updated 2 years ago
- Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more☆157Jan 11, 2026Updated 4 months ago
- Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.☆19Updated this week
- A platform for compiling, analyzing, and exploring tracking data☆50Feb 2, 2026Updated 3 months ago
- A tool for cell instance aware segmentation in densely packed 3D volumetric images☆125Updated this week
- ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy☆641Mar 29, 2026Updated last month
- The ImageJ plugin to run deep-learning models☆98Oct 28, 2025Updated 6 months ago
- An automated point-set based registration algorithm for correlative light and electron microscopy (CLEM)☆21Mar 12, 2026Updated 2 months 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.
- ☆14Jan 25, 2024Updated 2 years ago
- A first intoduction to scripting in Fiji using the ImageJ Macro language.☆27Sep 26, 2024Updated last year
- A minimal dependency napari plugin giving access to scikit-image functions☆23Mar 26, 2026Updated last month
- A template repo used to make new napari plugins☆37May 1, 2026Updated 2 weeks ago
- Morphological profiling using deep learning☆125Oct 19, 2024Updated last year
- Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for …☆14Apr 13, 2026Updated last month
- 3D shape analysis using deep learning☆31Oct 8, 2025Updated 7 months ago
- FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets☆30Apr 23, 2026Updated 3 weeks ago
- A napari plugin to view and edit layer metadata☆13May 1, 2026Updated 2 weeks 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.
- A self-explanatory, hands-on intro to bioimage analysis in python. Slightly outdated but still much liked by learners.☆99Feb 17, 2023Updated 3 years ago
- The known BioVoxxel Toolbox functions now improved for 2D and 3D images☆20Feb 10, 2026Updated 3 months ago
- This repository hosts notebooks, information and data for the Quantitative Bio-Image Analysis with Python Course 2022.☆17Nov 10, 2022Updated 3 years ago
- Open source Python library for building bioimage analysis pipelines☆198Updated this week
- Segment Anything for Microscopy☆680Updated this week
- Find profile pairs and compute retrieval metrics between them.☆22Apr 3, 2026Updated last month