Microscopy and image analysis educational resources to keep you learning and growing from home!

With many of us working from home, this is a terrific opportunity to expand our skillsets and increase our understanding of microscopy and/or image analysis. The online offerings listed below are primarily video-based tutorials or courses (biological microscopy-oriented).

A tip of the hat to Dr. Sara Parker (University of Arizona, Cellular & Molecular Medicine) for suggesting this page and for providing a number of the links. Dr. Parker is currently co-instructing CMM 542 "Fundamentals of Digital Imaging".


Optical Microscopy

iBiology is a very special resource with a number of video courses covering a wide range of topics in biological research besides microscopy and image analysis. iBiology's in-depth lectures on microscopy are taught often by the people who invented the technique, or other titans of microscopy. There is also a shorter list of videos for a microscopy overview course. Other interesting sources of material to learn can be found on the playlists shown at Imaging in Biology or Techniques.

Microcourses is a Youtube channel run by the folks from the Harvard Medical School light microscopy cores.

Molecular Expressions Microscopy Primer is not video based, but in spite of that it is a very deep resource on microscopy, specialty techniques, digital imaging, confocal microscopy, live cell imaging, and fluorescence. The articles were written by a number of well-known scientists and the JAVA tutorials are a fantastic way to learn about the variables of a particular topic. Similar websites include Nikon's MicroscopyU, Olympus' Microscopy Resource Center, Zeiss' Microscopy Online Campus, and Leica's Science Lab

MyScope is a series of interactive training modules covering a wide range of optical, electron and atomic force microscopy topics.

Image Analysis

ImageJ/FIJI - An interactive, self-paced tutorial on working with ImageJ/FIJI (Centre for Cell Imaging, University of Liverpool, UK). 

FIJI for Beginners and FIJI for Quantification - Youtube playlists from the Melbourne Advanced Microscopy Facility, University of Melbourne, Australia.

iBiology - Bioimage analysis overview (featuring ImageJ/FIJI and Cellprofiler) features six videos taught by Dr. Kevin Eliceiri (his LOCI group develops the ImageJ/FIJI plugins that allow us to open vendor-specific image files) and Dr. Anne Carpenter (her lab developed the popular open source software CellProfiler).

No Photon Left Behind has a number of video tutorials on FIJI/ImageJ, Imaris, and CellProfiler.

NEUBIAS (Network of European BioImage Analysts) will be putting many of their previous webinars online at their YouTube channel.

Have image analysis questions? Take a look at the Image.sc Forum. This site includes discussions on open source software such as ImageJ/FIJI, Python, CellProfiler, OMERO, and more.

Interested in learning about image manipulation ethics? The Office of Research Intergrity hosts the Online Learning Tool for Research Integrity and Image Processing. (Doug Cromey was a contributing author for this website)

Upcoming live online courses

Bioimage Analysis Course from the University of Helsinki - move fast, applications due 4/6! This course features one full day of image analysis education, followed by an a la carte full or half-day courses in FIJI, Imaris, Cell Profiler, and Zeiss’s ZEN software. 

NEUBIAS (Network of European Bioimage Analysts) is offering a series of image analysis and coding courses throughout April. Intro to Macro Language in ImageJ, Machine Learning, Icy (an open-source software initiative for bioimage analysis), and Quantitative Pathology. See also their YouTube channel.

The Royal Microscopy Society has a big list that includes educational offerings on a range of topics from companies, universities, and other networks.

Software

Adobe online training calendar (for the University of Arizona).

Computer Based Training at the University of Arizona - Free to UA faculty/staff/students. Online video courses covering a wide range of software, including Microsoft and Adobe products, software for graphics, video, audio, programming, operating systems, and much more. If you are interested in Microsoft specific certifications, there is also Microsoft's Imagine Academy.

Zeiss is making their ZEN software available (COVID-19 offer) for home use with a 90 day free license. You can download ZEN for free (your contact information will be requested). The modules included in the free ZEN download.

Leica is offering a 90 day free version of LAS X for download (COVID-19 offer).

Huygens is offering a temporary free version of the Huygens software for home use (COVID-19 offer). Huygens can deconvolve, visulaize and analyze image data.

Feeling ambitous? Consider Python for Microscopists, an extensive list of YouTube videos introducing this popular open source software that is used for image analysis (and many other things).

Techniques

Basic Principles of Clearing and Imaging Biological Tissues - Youtube recording of a webinar sponsored by Logos Biosystems.

BiteSizeBio has a number of free recorded webinars.

CYTO University has made a number of flow cytometry presentations and webinars available online (COVID-19 offer).

Physical sciences

Because not everyone is a biologist...

MyScope is a series of interactive training modules covering a wide range of optical, electron and atomic force microscopy topics.

EDAX has several years worth of recorded webinars on microanalysis.

GATAN also has a large number of recorded webinars on a wide range of materials science related topics.

A Collection of Atomic Force or Scanning Probe microscopy learning links from Dr. Massani

 
Created 04/06/2020, updated 04/14/2020. Creation of this web page was originally supported as part of the Southwest Environmental Health Sciences Center at the University of Arizona, NIEHS P30 ES006694.