Learning Bio-image Analysis
As suggested by the Image Analysis Collaboratory at Harvard Medical School.
Teaching Material and Notebooks
NEUBIAS’s Image Analysis Training Resources
Concepts, exercises, and solutions in MATLAB, ImageJ, Python, …not always all.
Bio-image Analysis Notebooks
Jupyter notebooks in Python.
Image Processing with Python: Summary and Setup
Using Python for basic image processing.
Books and Papers
Made to measure: An introduction to quantifying microscopy data in the life sciences
Covers image formation and analysis ina 2023 invited review.
A Hitchhiker`s Guide through the Bio-image Analysis Software Universe
2022 overview article on bioimage analysis software. A more detailed is of software is available here.
Introduction to Bioimage Analysis
Self-contained online book for hands-on training with examples in Fiji and Python, targetted towards life scientists with insane production value.
Videos
EPFLx: Image Processing and Analysis for Life Scientists
Basic image analysis for life scientists with a non-engineering backgroun (Self-guided course).
NEUBIAS on YouTube
Growing list of ~1 hour introductions to individual tools and methods.
Global BioImaging: Image Analysis & Visualization
Many hours for CellProfiler, Fiji, Imaris.
COBA: Center for Open Bioimage Analysis
YouTube playlists for intros, workshops, software.
Robert Haase’s videos
Concepts and software: Fiji, CellProfiler, Icy, Knime, Python.
Microcourses
Short videos on microscopy concepts—useful for understanding image formation.
Johanna M. Dela Cruz
Collection of short how-to videos for specific analysis steps in FIJI (ImageJ).
Halfway to I2K 2023
Collection of all the workshops from Halfway to I2K 2023.
Miscellaneous
Awesome Biological Image Analysis
Large list of GitHub repositories of BIA tools.
BioImage Informatics Index
BioImage analysis tools database.
FocalPlane
To stay updated, once you have learned.
And for everything else, there is The Forum.
