A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
☆180Mar 14, 2026Updated last month
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 2 months ago
- Gamified image segmentation quality estimation☆19May 1, 2025Updated 11 months ago
- ☆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 4 months ago
- An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code.☆91Mar 24, 2026Updated 3 weeks ago
- 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.
- Lecture materials "Bio-image analysis, biostatistics, programming and machine learning for computational biology" at the Center of Molecu…☆234Sep 11, 2023Updated 2 years ago
- Non-comprehensive list of projects and resources related to open microscopy.☆177Mar 19, 2026Updated last month
- Single cell Morphology Quality Control (coSMicQC)☆11Apr 9, 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☆18Updated this week
- ☆52May 1, 2025Updated 11 months ago
- Guides and code for 3D nuclear instance segmentation☆23Dec 2, 2025Updated 4 months ago
- An introduction to bioimage analysis - http://bioimagebook.github.io☆76Feb 5, 2026Updated 2 months ago
- A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)☆20Updated this week
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more☆154Jan 11, 2026Updated 3 months ago
- Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.☆18Updated this week
- A platform for compiling, analyzing, and exploring tracking data☆50Feb 2, 2026Updated 2 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☆636Mar 29, 2026Updated 3 weeks ago
- The ImageJ plugin to run deep-learning models☆97Oct 28, 2025Updated 5 months ago
- An automated point-set based registration algorithm for correlative light and electron microscopy (CLEM)☆21Mar 12, 2026Updated last month
- ☆14Jan 25, 2024Updated 2 years ago
- A first intoduction to scripting in Fiji using the ImageJ Macro language.☆27Sep 26, 2024Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- A minimal dependency napari plugin giving access to scikit-image functions☆23Mar 26, 2026Updated 3 weeks ago
- A template repo used to make new napari plugins☆37Updated this week
- Morphological profiling using deep learning☆124Oct 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 week
- 3D shape analysis using deep learning☆31Oct 8, 2025Updated 6 months ago
- FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets☆29Updated this week
- A napari plugin to view and edit layer metadata☆13Updated this week
- 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 2 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.
- Open source Python library for building bioimage analysis pipelines☆196Updated this week
- This repository hosts notebooks, information and data for the Quantitative Bio-Image Analysis with Python Course 2022.☆17Nov 10, 2022Updated 3 years ago
- Segment Anything for Microscopy☆673Apr 8, 2026Updated last week
- Find profile pairs and compute retrieval metrics between them.☆22Apr 3, 2026Updated 2 weeks ago
- ☆19Feb 27, 2020Updated 6 years ago
- A place to collect information used in lectures, demos, workshops, etc.☆17Sep 26, 2024Updated last year
- A napari plugin for clustering objects according to their properties.☆90Updated this week