awesome-scientific-image-analysis
github.com/epfl-center-for-imaging/awesome-scientific-image-analysis ↗Scientific image analysis resources and software tools.
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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.
🛸 Other
- aicsimageio🛠️ Utilities
Image reading and metadata conversion.
- 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.
🧩 OME-Zarr
- An Introduction to OME-Zarr for Big Bioimaging DataLearning resources
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.
- NeuroglancerSoftware tools
Browser-based visualizations compatible with large images (zarr).
- OME-NGFF ValidatorSoftware tools
Validate an OME-NGFF file.
- VivSoftware tools
Multiscale visualization in the browser.
🏗️ 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.
- Hugging Face Spaces
Build, host, and share ML apps.
- Imaging Server Kit
Run image processing algorithms via a web API.
🔍 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).
- OpenPifPafPose estimation
Human pose estimation.
- RS-FISHSpots
Spot detection in 2D and 3D images in Fiji.
🔬 Fiji (ImageJ)
- BigStitcherPlugins
Stitching for large images.
- Bio-FormatsPlugins
Import data from many life sciences file formats.
- DeepImageJPlugins
Run deep learning models in Fiji.
- FFmpegPlugins
Load videos into Fiji.
- Image handling using Fiji - training materialsLearning resources
Joanna Pylvänäinen.
- MorphoLibJPlugins
Morphological operations.
🔖 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.
🪄 Image denoising
- CAREamicsSoftware tools
Deep-learning based, self-supervised algorithms: Noise2Void, N2V2, etc.
- CellPose3 - OneClickSoftware tools
Deep-learning based denoising models for fluorescence and microscopy images.
- CSBDeepSoftware tools
Access CSBDeep based tools in Fiji.
- Denoising a pictureLearning resources
Tutorial from the Scikit-image website.
- NoiseLearning resources
Chapter from the Introduction to Bioimage Analysis handbook.
- noise2selfSoftware tools
Blind denoising with self-supervision.
Showing a sample of 195 resources. View the full list on GitHub →