Image Analysis Training Material
Our Courses and Workshops
“Incorporating Machine learning tools into image analysis workflows using Fiji Ilastik and Stardist” Workshop
Here is all the Workshop Material including Presentation, detailed Exercises, related Scripts and Sample data (May 2023)
“Image Analysis with QuPath” Workshop
Here is all the Workshop Material including Presentation, detailed Exercises, related Scripts and Sample data (March 2023).
It is also available on our Github (except for the full slide image, which is too big)
“Practical Image Analysis for Biology” Course
between 2015-2019 we taught once a year a course on "Practical Image Analysis for Biology" at the Feinberg School at Weizmann
The course team is: Ofra Golani, Vyacheslav (Slava) Kalchenko, Reinat Nevo, Sefi Addadi
You can access the All the 2018 course material, or parts of it:
Lectures (2018 edition)
Hands-on exercises on Image Analysis basics using ImageJ/Fiji (2018 edition), best to do while going over lectures of Day1-3, (2019 Edition , with extra exercises)
Hands-on exercises for ImageJ/Fiji macro writing , best to do while going over lecture slides of Day6-8
Hands-on exercises for learning Imaris (2019, for Imaris 9.3.1)
We gave a shorter Image analysis workshop at the ISM-2017 meeting based on the the first part of our course.
NEUBIAS Academy@Home
NEUBIAS Academy is a new initiative, aimed to provide sustainable material and activities focused on Training in Bioimage Analysis
Webinars recordings are available on Youtube NEUBIAS Channel, and a thread per event is opened in the image.sc Forum to report Q&As and to welcome further questions/comments.
Some of the webinars are linked below individually , but there are many more on the You Tube channel
Defragmentation Training School (2022) - by NEUBIAS Academy & EOSC-Life - Recordings of the course lectures are on Youtube NEUBIAS Channel
See also: Bioimaging data analysis: The favorite imaging analysis tools of Neubias members
Imaging & Microscopy “My Favorite Tools” series
Image Ethics & Reproducable imaging & image analysis
Kota Miura’s lecture at NEUBIAS Academy
“Reproducible image handling and analysis” by Kota Miura, Simon F Nørrelykke, The EMBO Journal (2021)40:e105889
“A guide to accurate reporting in digital image acquisition – can anyone replicate your microscopy data?” by John M. Heddleston, Jesse S. Aaron, Satya Khuon and Teng-Leong Chew
Online Courses and Image Analysis Training Material
MOOC on Bioimage Analysis by the EPFL team (You need to enroll, but it is free)
Introduction to BioImage Analysis with Fiji by Robert Haase, from Biotechnology Center of the TU Dresden and center for systems biology Dresden, which include also ImageJ macro-writing lectures. It is a course in process, so lectures are added every week. (videos, slides, catch-up code)
iBiology BioImage Analysis Course (videos)
Course material on Introduction to Image Analysis, mainly focused on Fiji by the Scientific Computing Facility (SCF) of the Max Planck Institute for Cellular Biology and Genetics (MPI-CBG) in Dresden
Image Analysis with Fiji, Intermediate Image Analysis by Jeremey Pike
Recordings of workshops given at “From Images to Knowledge 2020”
Image.sc forum is a great resource and community for any bioimage analysis related question.
See also this thread about IA training material
Open access textbooks on Image Analysis
Image Analysis Basics using ImageJ/Fiji
"Basics of Image Processing and Analysis" by Kota Miura
"Workshop: Image Processing and Analysis with ImageJ ", By Volker Baecker
Advanced material covering ImageJ/Fiji Macro writing, Matlab and Workflows
"Though many textbooks titled "biological (or medical) image processing" could be found in bookstores, these textbooks mostly focus on how image processing algorithms are working and do not explain the detailed steps to apply them for individual biological research projects. The textbook will try to cover this missing part, by providing detailed explanations and example workflows of combining various image processing algorithms to construct practical workflows using scripting."
"Computer Optimized Microscopy, Methods and Protocols", edited by Elena Rebollo and Manel Bosch
"Macro Programming in ImageJ", by Kota Miura
"ImageJ Macro Programming for Biological Image Analysis" by Volker Baecker
Fiji plugins tools
MorphoLibJ: https://www.youtube.com/watch?v=_SiM33C3KcE
3D ImageJ suite: https://www.youtube.com/watch?v=OPC2kP-5By4
GPU acceleration / CLIJI2: https://www.youtube.com/watch?v=uMj0OS1TiQE
TrackMate:
QuPath
is open source software for bioimage analysis. It is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images - but it can be applied to lots of other kinds of image as well.
Features include: Powerful annotation & visualization tools, Built-in algorithms for common tasks, including cell and tissue detection, Interactive machine learning, both for object and pixel classification, Multiplexed analysis
NEUBIAS QuPath webinar:
Running a complex project in QuPath Tutorial by Sara McArdle and Zbigniew Mikulski
Recording of extensive hands-on training workshop of QuPath From Samples to Knowledge 2020 is available online with exercises and training material.
QuPath for Multiplexed Fluorescence Microscopy by Anna Klemm :
I2K-2022: QuPath for Fiji users
NEW: QuPath Training Course From Samples to Knowledge 2023
Image Analysis using Python
Image Processing with Python course by Guillaume Witz and David Haberthür from Science IT Support unit at Bern University
Python for BioImage Analysis course organized by Dominic Waithe, Gabriella Rustici, Chas Nelson and Stephen Cross
Python for Microscopists videos by Sreeni
Napari
Napari:
Machine Learning and Deep Learning for Image Analysis
ML basics (Robert Haase): ,
WEKA+LabKit (Robert Haase):
Ilastik basics (Robert Haase):
Ilastik Tutorial (Anna Kreshuk, FOM 2021):
Ilastik advanced
Intro + DeepImageJ:
StarDist:
ZeroCostDL4Mic:
QuPath: , see QuPath section above for more material
CARE:
Cellpose: Recording coming soon at NEUBIAS YouTube, I2K-2022 workshop: train you own models with Cellpose2.0
Microscopy Training Material
iBiology Microscopy Course (Videos)
Microcourses : short (10-15 min) educational microscopy videos by Nikon Imaging Center @ Harvard medical school