awesome-scientific-image-analysis
github.com/epfl-center-for-imaging/awesome-scientific-image-analysis ↗Scientific image analysis resources and software tools.
Use this list with your AI agent
Add the Context Awesome MCP server to Claude, Cursor, or any MCP client, then ask:
"Show me papers resources from awesome-scientific-image-analysis"
Installation instructions →What's inside
📚 Learning resources
- 2022 - A Hitchhiker's guide through the bio-image analysis software universePapers
Robert Haase et al.
- 2023 - Towards effective adoption of novel image analysis methodsPapers
Talley Lambert, Jennifer Waters.
- 2024 - Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutionsPapers
Beth Cimini.
- Awesome Biological Image AnalysisCurated lists
Image analysis techniques for biological research.
- Awesome Computer VisionCurated lists
Algorithms and tools for machine vision.
- Awesome Medical ImagingCurated lists
Research tools for medical imaging.
🌻 Visualization
- 3DscriptFiji-based tools
Render 3D animations in Fiji.
- 3D ViewerFiji-based tools
Basic 3D image viewer.
- BigDataViewerFiji-based tools
3D viewer optimized for large data sets.
- fastplotlibPython-based tools
Fast plotting library running on WGPU.
- itkwidgetsPython-based tools
VTK viewer in Jupyter notebooks.
- K3D-jupyterPython-based tools
Jupyter Notebook 3D visualization package.
🧩 OME-Zarr
- An Introduction to OME-Zarr for Big Bioimaging Data
Theory and practice of using the OME-Zarr format.
- fileglancerSoftware tools
Browse, share, and publish OME-Zarr data.
- FractalSoftware tools
Framework to process bioimaging data at scale in the OME-Zarr format.
- NeuroglancerViewers
Browser-based visualizations compatible with large images (zarr).
- NgioSoftware tools
Python library to work with OME-Zarr files.
- OME-NGFF ValidatorSoftware tools
Validate OME-NGFF files.
🏗️ Infrastructure
- BAND
Bioimage ANalysis Desktop.
- BioImage.IO dev
Models, Datasets, and Applications for bioimage analysis.
- BIOP-desktop
Virtual desktop for bioimage analysis.
- Galaxy (EU)
Web-based platform for accessible computational research.
- Imaging Server Kit
Run image processing algorithms via a web API.
- Nextflow
Create scalable and reproducible workflows.
🛸 Other
- bia-bob🤖 LLMs
LLM-based assistant for interacting with image data.
- BioImage.IO Chatbot🤖 LLMs
AI assistant specialized in bioimaging.
- bioio🛠️ Utilities
Read, write, and manage microscopy images.
- Camera Calibration🏁 Camera calibration
First Principles of Computer Vision (video format).
- Cameras and Lenses📷 Image acquisition
Bartosz Ciechanowski.
- COLMAP🍄 Photogrammetry
Structure-from-motion and multi-view stereo.
🔍 Object detection
- Big-FISHSpots
smFISH spot detection and analysis in Python.
- C4W3L09 YOLO AlgorithmLearning resources
Introduction to YOLO by Andrew Ng (video format).
- DeepLabCutPose estimation
Animal pose estimation.
- Detecting BlobsLearning resources
First Principles of Computer Vision (video format).
- nnDetectionBounding boxes
Self-configuring framework for 3D bounding box detection.
- OpenPifPafPose estimation
Human pose estimation.
🔬 Fiji (ImageJ)
- BigStitcherFiji plugins
Stitching for large images.
- Bio-FormatsFiji plugins
Import data from many life sciences file formats.
- DeepImageJFiji plugins
Run deep learning models in Fiji.
- FFmpegFiji plugins
Load videos into Fiji.
- Image handling using Fiji - training materials
Joanna Pylvänäinen.
- MiCFiji plugins
Compute metrics (TP, FP, FN, Jaccard index...) on segmentation masks.
🔖 Getting started
- bioimagingguide.org
Center for Open Bioimage Analysis.
- CellProfiler
Open software for automated quantification of biological images.
- Fiji
ImageJ, with “batteries-included”.
- First Principles of Computer Vision
Columbia University.
- Image data science with Python and Napari
EPFL & TU Dresden.
- Image Processing and Analysis for Life Scientists
BIOP, EPFL.
Showing a sample of 195 resources. View the full list on GitHub →