Useful resources for learning data analysis and visualization

Image Analysis

• Lecture BioImage Analysis 2020 by Robert Haase at Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
  • Introduction to bio-image analysis with Fiji, images, pixels, measurements
    • Part 1: https://www.youtube.com/watch?v=e-2DbkUwKk4
    • Part 2: https://www.youtube.com/watch?v=Akedfyp5AxY
  • Filters + Image segmentation (using Fiji in Part 2)
    • Part1: https://www.youtube.com/watch?v=LT8L3vSLQ2Q
    • Part2: https://www.youtube.com/watch?v=08SZnZBl4lM
  • Feature extraction
    • https://www.youtube.com/watch?v=dria4wCiaz0
  • Introduction to ImageJ macro programming: Variables and operations
    • https://www.youtube.com/watch?v=q4ISEWq6q4E
  • ImageJ macro programming: ROIs and Overlays
    • https://www.youtube.com/watch?v=IaY2zNKrtYg
  • ImageJ macro programming: Functions, Arrays, Plots and Tables
    • https://www.youtube.com/watch?v=Ydk6z-M9bAc
  • ImageJ macro programming: User Interfaces
    • https://www.youtube.com/watch?v=JncZoA-Afk4
  • Writing good code
    • https://www.youtube.com/watch?v=gSBR34m1OCE
• NEUBIAS Academy
  • A series of online events targeting Bioimage Analysis Technology
    • https://mailchi.mp/dbe1596fccf7/neubias-academy-starts-up
    • http://eubias.org/NEUBIAS/training-schools/neubias-academy-home/
  • [Archives] https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg
• IAFIG-RMS Python for Bioimage Analysis Course (2019)
  • https://github.com/IAFIG-RMS/Python-for-Bioimage-Analysis
• Fiji/ImageJ
  • ImageJ/Fiji Macro Language https://www.youtube.com/watch?v=o8tfkdcd3DA
• Annotation
  • Quantitative Pathology & BioImage Analysis: QuPath https://www.youtube.com/watch?v=4An5n6Y_rRI
• Python for Microscopists by Sreeni
  • https://www.youtube.com/channel/UC34rW-HtPJulxr5wp2Xa04w/videos

Visualization

• Plotting anything with ggplot2 (Part 1) by Thomas Lin Pedersen at RStudio (2020)
  • The underlying theory of ggplot2 and how it is reflected in the API
  • Part 1: https://www.youtube.com/watch?v=h29g21z0a68
  • Part 2: https://www.youtube.com/watch?v=0m4yywqNPVY
    • Introducing patchwork, gganimate, ggrepel, ggforce, ggraph, tidygraph, hrbrthemes, ggthemes packages
  • [Materials] https://github.com/thomasp85/ggplot2_workshop

Microscopy

• Microcourses
  • Microcourses are short educational videos on a variety of light microscopy topics, brought to you by a team of microscopists from Harvard Medical School.
  • https://www.youtube.com/channel/UC4cOKa0TZK8CQhzSQqfwuMQ

Machine Learning

• Interactive Tools for ML, DL and Math
  • https://github.com/Machine-Learning-Tokyo/Interactive_Tools

Misc.

• The Missing Semester of Your CS EducationThe Missing Semester of Your CS Education
  • The shell, Shell Tools and Scripting, Editors (Vim), Data Wrangling, Command-line Environment, Version Control (Git), Debugging and Profiling, Metaprogramming, Security and Cryptography, and Potpourri
  • https://missing.csail.mit.edu