As suggested by the Image Analysis Collaboratory at Harvard Medical School

Papers

• Made to measure: An introduction to quantifying microscopy data in the life sciences
  • 2023 invited review
  • Covers image formation and analysis
• A Hitchhiker`s Guide through the Bio-image Analysis Software Universe
  • 2022 overview article
  • Downloadable spreadsheet with more IA software

Websites

• 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

Online books

• Introduction to Bioimage Analysis
  • Self-contained online book for hands-on training with examples in Fiji and Python
  • Target audience: Life scientists
  • Production value: insane!
• Quantitative Bioimaging
  • Companion website to paper “A biologist’s guide to the field of quantitative bioimaging”

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.

Essential Image Analysis Software tools