Image Analysis Training Material

Owned by Ofra Golani
Last updated: Nov 27, 2023
4 min read

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:

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

F1000 NEUBIAS gateway

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: Advanced Image Processing with MorphoLibJ - [NEUBIASAcademy@Home] Webinar

3D ImageJ suite: Introduction to 3D Analysis with 3D ImageJ Suite [NEUBIAS Academy@Home] webinar

GPU acceleration / CLIJI2: GPU-accelerated Image Processing with CLIJ2 - [NEUBIASAcademy@Home] Webinar

TrackMate: Tracking cells and organelles with TrackMate - [NEUBIAS Academy@Home] Webinar

 

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: Quantitative Pathology & BioImage Analysis: QuPath - [NEUBIASAcademy@Home] 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 : Introduction to QuPath for Multiplexed Fluorescence Microscopy

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: Multi-dimensional image visualization in Python using napari [NEUBIAS Academy@Home] webinar

Machine Learning and Deep Learning for Image Analysis

ML basics (Robert Haase): 08a Machine Learning for Pixel and Object Classification ,

WEKA+LabKit (Robert Haase): 08b Machine Learning for Pixel Classification in Fiji

Ilastik basics (Robert Haase): 08c Machine Learning for Pixel and Object Classification in ilastik

Ilastik Tutorial (Anna Kreshuk, FOM 2021): Tutorial Image Analysis with Machine Learning Basic Principles and Examples Using Ilastik 28 03 202

Ilastik advanced ilastik beyond pixel classification - [NEUBIASAcademy@Home] Webinar

Intro + DeepImageJ: Intro to Machine Learning-DeepLearning-DeepimageJ - [NEUBIASAcademy@Home] Webinar

StarDist: Introduction to nuclei segmentation with StarDist - [NEUBIASAcademy@Home] Webinar

ZeroCostDL4Mic: ZeroCostDL4Mic - [NEUBIAS Academy@Home] Webinar

QuPath: https://www.youtube.com/watch?v=4An5n6Y_rRI ,  see QuPath section above for more material

CARE: https://www.youtube.com/watch?v=ipp0mxfjhwY

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