Preparing image for scientific publications (Fiji, Illustrator)

  1. Figure Preparation Ethics (How to not get your paper retracted): https://www.youtube.com/watch?v=sYlj7G0FLtc&list=PLukoMywfuxHJ4pRhEtcTjPyCm89Q0mTsH
  2. Scientific Figure Preparation in Adobe Illustrator and Fiji – Part 1: Getting Started: https://www.youtube.com/watch?v=3IwngW58mJI
  3. Scientific Figure Preparation in Adobe Illustrator and Fiji – part 2: Image Data: https://www.youtube.com/watch?v=VMxHKNs1kpU
  4. Scientific Figure Preparation in Adobe Illustrator and Fiji – Part 3: Layout: https://www.youtube.com/watch?v=y59gBEPz6yg
  5. Scientific Figure Preparation in Adobe Illustrator and Fiji – Part 4: Text: https://www.youtube.com/watch?v=0V6qP_kgfPE
  6. Scientific Figure Preparation in Adobe Illustrator and Fiji – part 5: Charts and Graphs: https://www.youtube.com/watch?v=iyO1wSbvtu0
  7. Scientific Figure Preparation in Adobe Illustrator and Fiji – part 6: Color: https://www.youtube.com/watch?v=CxBhi1dghP0

General microscopy

  1.  iBiology collection of videos about all aspects of microscopy
    • Microscopy
    • All levels
    • Freely accessible
    • Video
  2. iBiology collection of videos about main aspects of bioimage analysis
    • Bioimage processing
    • All levels
    • Freely accessible
    • Video
  3. Interactive course on a large variety of microscopy techniques
    • Methods in microscopy
    • All levels
    • Freely accessible
    • Interactive course
  4. Microscopy teaching materials (Karolinska Institute)
    • Microscopy techniques
    • All levels
    • Freely accessible
    • Online materials
  5. Tutorial: guidance for quantitative confocal microscopy
    • Quantitative confocal microscopy
    • All levels
    • Access to Nature required
    • Paper
  6. Course on cryo-EM and 3D-EM (CalTech)
    • Cryo-Electron Microscopy
    • Beginner
    • Freely accessible
    • Interactive course
  7. Octopus Webinar Series
    • Fluorescence imaging and correlative light and electron microscopy
    • Advanced
    • Freely accessible, registration required
    • Webinars

Image processing & Visualization

Fiji / ImageJ

  1. Introduction to Fiji (University of Bern)
    • Fiji intro
    • Beginner
    • Freely accessible
    • Slides
  2. 30 Minutes introduction to Fiji
    1. Fiji Intro
    2. Beginner
    3. Freely accessible
    4. Video
  3. Complete intro to Fiji (University of Liverpool)
    • Fiji intro
    • Beginner
    • Freely accessible
    • Slides
  4. MOOC course on bio image processing with Fiji (EPFL)
    • Fiji intro
    • Beginner
    • Free with EdX registration
    • Interactive course
  5. (Bio)image processing introduction
    • Fiji intro
    • Beginner (under development as of April 2020)
    • Freely accessible
    • Video
  6. Neubias webinar series
    • All aspects of Image processing, mostly BioImaging but also deep learning, ethics, …
    • Beginnner to advanced
    • Freely accessible, registration required
    • Live streaming webinar

Python

  1. Python course on image processing I (University of Bern)
    • Python intro for image processing
    • Beginner (non programmers)
    • Freely accessible
    • Slides
  2. Python course on image processing II (University of Bern)
    • Python intro for image processing
    • Mid-level to advanced
    • Freely accessible
    • Online programming
  3. Python tutorials for microscopists with no coding skills
    • Python intro for image processing
    • Beginner
    • Freely accessible
    • Video
  4. Python for Bioimage Analysis
    • Python intro for image processing
    • All levels
    • Freely accessible
    • Online programming
  5. General Python course
    • Python intro
    • All levels (zero to hero)
    • Freely accessible
    • Online programming

Data science

  1. Amira-Avizo learning center
    1. Learning tools for Avizo
    2. Beginner ot advanced
    3. Freely accessible
    4. Video
  2. Online R primer for beginners
    • Intro in R using RStudio
    • Beginner
    • Freely accessible
    • Online tutorial
  3. Online R course (Harvard)
    • All aspects of R
    • Beginner to advanced
    • Freely available, registration required
    • Online tutorial
  4. Coursera course on Matlab programming (VanderBild University)
    • Intro on Matlab
    • Beginner
    • Freely accessible, registration required
    • Online materials
  5. Coursera course on Machine learning (Stanford University)
    • Intro on Machine Learning
    • Beginner
    • Freely accessible, registration required
    • Online materials

Commercial resources

  1. Microscopy University: Online course for information on all light microscopy methods
    • Methods in microscopy
    • Nikon
    • All levels
    • Freely accessible
    • Online tutorials
  2. Arivis Webinar Series
    • Each Thursday: Free Webinar Series on Image Visualization & Analysis across Microscopy Methods
    • Arivis
    • All levels
    • Freely accessible, registration required
    • Webinars
  3. School of fluorescence
    • Fluorescence microscopy
    • ThermoFischer
    • All levels
    • Freely accessible
    • Online materials
  4. Time-resolved microscopy
    • Time-resolved microscopy
    • Picoquant
    • Advanced levels
    • Freely accessible, registration required
    • Webinars
Thanks to Dr Guillaume Witz, University of Bern