The image analysis field guide

Essential toolkit to get started in scientific image analysis.

Welcome! Use this field guide to quickly find the information you need to tackle your scientific image analysis challenges.

🔖 Getting started

These are our favourite resources for learning the basics of image analysis:

Image data science with Python and Napari @EPFL

https://biapol.github.io/Image-data-science-with-Python-and-Napari-EPFL2022/intro.html

Image Processing and Analysis for Life Scientists

https://courseware.epfl.ch/courses/course-v1:EPFL+IPA4LS+2019_t3/about

Introduction to Bioimage Analysis

https://bioimagebook.github.io/README.html

Here’s a short list of image analysis software that we recommend:

Fiji

https://fiji.sc/

Ilastik

https://www.ilastik.org/

Napari

https://napari.org/

QuPath

https://qupath.github.io/

Read our setup guide:

Setting up Python for scientific image analysis

./sections/python/notebooks/python_setup.html

🚀 Explore topics

Tip

Use Ctrl+K to search this site!

Delve deeper into individual topics.

Image segmentation

./sections/image_segmentation/index.html

Image registration

./sections/image_registration/index.html

Image denoising

./sections/image_denoising/index.html

Object detection and tracking

./sections/detection_and_tracking/index.html

Image data visualization

./sections/image_data_visualization/index.html

Performance optimization

./sections/performance_optimization/index.html

💡 Example projects

Launch the notebooks

If you are in EPFL, you can launch the notebooks to run them interactively on our Jupyter Hub by clicking on the rocket icon at the top of a notebook page.

Browse our collection of example image analysis projects done in collaboration with EPFL labs and presented as Jupyter notebooks.

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🧑‍🤝‍🧑 Join the community

If you are in EPFL, you can join our Matrix server by connecting to element.epfl.ch.

Contribute

Read our guide to find out how you can contribute to our project.

https://github.com/EPFL-Center-for-Imaging/image-analysis-field-guide/blob/main/CONTRIBUTING.md

Feedback

Please fill-in our feedback form. We’d love to hear your opinion about our site!

https://forms.gle/toHAP2ydydXBCndGA

Image.sc

Our favourite online forum on image analysis.

https://image.sc/