Paula Andrea Martinez
Paula Andrea Martinez National Training Coordinator - Characterisation Community

Publicly accessible software tutorials

Publicly accessible software tutorials

A list of publicly accessible tutorials with a short description.

A list of publicly accessible tutorials with a short description. We will appreciate if you can curate and/or add to this list.

Last updated 10 June, 2020.

Tutorials from external resources

List of tutorials ordered alphabetically.

Microscopy

Computational Bioimaging

From images (both light and electron microscopy) to data. This course will cover the process of dealing with microscopy data, converting between formats, analysing images in a clear and reproducible fashion and preparing images for publication. Includes FIJI, Python and OMERO. By Matthew Hartley 2015, from John Innes Centre, JIC. Online tutorial. Labeled for beginners in microscopy analysis.

FIJI

Neurosciences

FreeSurfer

  • If you want to learn FreeSurfer the documentation is ready to be explored.

fMRI

  • Intro to fMRI by Berkeley.

MRtrix

Various tutorials from OHBM

The organisation for Human Brain Mapping (OHBM) has a public library of the latests annual meeting materials, including videos of talks and courses.

Generic Software tools

Git

  • Git for Scientists by Miles McBain 2019. A 3.5 hour introduction to basic shell and git/GitHub. Read and follow along the tutorial here.
  • Git for curious.

Image Data Resource

  • The Image Data Resource (IDR) publishes “reference image” datasets supporting conventional peer-reviewed publications and integrates them with other imaging datasets for cross-dataset querying of metadata (e.g. genes, phenotypes, small molecules) and re-analysis. Submission of datasets to IDR and an IDR metadata example.

OMERO

Python

Last updated 10 June, 2020

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