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.
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.
- OMERO + FIJI From GBI Sydney, Sep 2018. FIJI analysis starts on page 10. Author: Petr Walczysko part of Hands-on data management with OMERO.
- ImageJ tutorials from ImageJ.net.
- ImageJ tutorials using Jupyter notebooks. This project contains example code for working with ImageJ and SciJava. CC0 1.0 Universal license.
- FIJI manual by Cameron Nowell and images.
- Using ImageJ CC0 1.0 Universal license.
- Practical exercises to learn image analysis using ImageJ/Fiji with a strong focus on biological fluorescence microscopy data Author: Christian “Tischi” Tischer, 2018 and 2019. Suggested to look at folders handouts and practicals.
- Fiji scripting tutorial using python (jython) by Albert Cardona.
- ImageJ and FIJI by Peter Bankhead.
- Getting started with the plugin TrackMate.
- A very fast way to make tutorials in FIJI and upload them to the FIJI Wiki.
- A brief introduction to machine learning for bio-imaging accessible to download from http://bit.do/ML-Imaging-WS provided by Nick Hamilton, Sep 2018 and March 2019.
- Using FIJI with Trainable Weka from imageJ.net.
- Counting neurons in brain slices with FIJI by Delane Espinueva; or two ways to count cells with ImageJ by Christine Labno.
- Introduction to Image processing video from the Institute for Molecular Bioscience by Nicholas Condon.
- Fluorescence Lifetime Imaging Microscopy video from the Institute for Molecular Bioscience by Nicholas Condon.
- If you want to learn FreeSurfer the documentation is ready to be explored.
- Intro to fMRI by Berkeley.
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 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.
- Open Microscopy Training OMERO and OMERO help.
- Introductory talk about OMERO Dundee Workshop 10 June, 2019.
- OMERO it redirects to https://code.research.uts.edu.au/MIF/OMERO-instructions/wikis/home.
- Python basics by Berkeley.
Last updated 10 June, 2020