On The Web

Here are links to some of Micrographia@Western’s favorite web-based resources for microscopy. This includes everything from protocol sites, to key papers, to software, to YouTube channels. Please contact us if you have a resource you think should be shared on this page.


Image Analysis Software

FIJI. This is one of the most commonly used image analysis programs. This is based on ImageJ, but has a series of plugins and add-ons preinstalled, plus an update system, making it more user friendly and more functional out-of-the-box. FIJI is easily extendable by plugins, and is capable of working with other software packages (e.g. Matlab), FIJI is a powerful image analysis package. Even better – its FREE!

ImageJ. This is the software underlying FIJI. ImageJ can be installed instead of FIJI, or run separately beside FIJI. As ImageJ has no preinstalled plugins or add-ons, it can be customized for your specific needs. As with FIJI, ImageJ is FREE!

QuPath. This software allows for you to train a machine learning algorithm to analyze tissue sections and other fluorescence and histological images. A properly trained algorithm can automatically identify and phenotype cells in images, saving you hundreds of hours of manual annotation. This program too is FREE!

Don’t forget to check out their From Zero to QuPath Hero! YouTube series to get a quick start on using QuPath.

Cell Profiler. This software allows you to design automated analysis pipelines to speed the analysis of your micrographs. Capable of procedures such as cell segmentation, tracking, and classification, this powerful tool can speed your analysis. They have also added a new machine learning extension (CellProfiler Analyst) which enables even more complex analyses of your images. These programs are FREE!

Imaris. This is a closed-source analysis platform capable of advanced image analysis procedures including 3D cell tracking, advanced 3D/4D rendering, cell segmentation, and other image analysis tasks.

Image-Pro. This is a closed-source analysis platform featuring a range of AI and conventional tools for 2D and 3D image analysis and visualization.


YouTube Channels

Johanna M. Dela Cruz’s channel contains numerous excellent tutorials on how to perform a range of image analyses using FIJI software.

The Perfect PSF – SW Ontario’s own Dan Stevens’ YouTube channel contains excellent tutorials on image acquisition and processing using Zeiss’ Zen software.

Microcourses does deep dives into microscopy concepts, providing the viewer with an excellent foundation on the theory and practice of microscopy.

Dr Florian Ströhl’s channel about optical elements and methods: what they do, how they work, and how to use them properly.

Open UC2 – a 3D printable DIY microscope capable of being configured for multiple purposes.


Books and Papers

Fluorescent Microscopy contains a collection of protocols ranging from basic immunostaining through to intravital and super-resolution methods. Edited by Micrographia@Western’s own Bryan Heit.

This is a must-read for all microscopists who want to avoid inadvertently performing inappropriate modifications to their images. Data integrity is critical to microscopy, and this is an excellent primer and what can – and should not – be done when manipulating images.

Mike Rossner, Kenneth M. Yamada; What’s in a picture? The temptation of image manipulationJ Cell Biol 5 July 2004; 166 (1): 11–15. doi: https://doi.org/10.1083/jcb.200406019

This is a must-read for anyone wanting to do live-cell microscopy. Common errors and their correction, as well as best practices, are discussed.

Melanie M. Frigault, Judith Lacoste, Jody L. Swift, Claire M. Brown; Live-cell microscopy – tips and toolsJ Cell Sci 15 March 2009; 122 (6): 753–767. doi: https://doi.org/10.1242/jcs.033837

The Handbook of Biological Confocal Microscopy is one of the most important books published on biological microscopy. This heave tome starts with foundational concepts on how microscopes and fluorophores work, then moves into basic microscopy approaches, and later delves into complex and highly specialized methodologies. A must-read for any serious microscopist.

Do you know the limitations of your microscope? Or how noise affects your quantitation? This paper addresses these, and other limitations, that affect our ability to perform quantitative analyses on micrographs.

Jennifer C. Waters; Accuracy and precision in quantitative fluorescence microscopyJ Cell Biol 29 June 2009; 185 (7): 1135–1148. doi: https://doi.org/10.1083/jcb.200903097

Micrographia. Published by Robert Hooke in 1665, this book was the first major publication to focus on microscopy. In it, Hooke made the first description of cells, launching the science of cell biology. Hooke also made interesting observations on the structure of plants and insects, and even turned his optics to the skies, an in this book published some of the first high resolution images of craters on the moon. As the name suggests, this book is foundational to Micrographia@Western, and to modern microscopy in general.

A free version of Micrographia is available from the Gutenberg Project.

A beautiful replica, complete with the fold-out images of the original, is available for purchase from the Folio Society.


Other Resources

The Microscopical Society of Canada is Canada’s largest organization dedicated to microscopy-based research. Conferences, awards, and student resources are all available via the MSC.

Canada Bioimaging is an organization dedicated to building a community of image analysists with expertise in analysis of biological samples.

BioImaging North America is a network of experts from across North America who specialize in various forms of bioimaging, including microscopy.

FPbase is THE source for finding spectra, FRET overlap, QE, and other information for fluorescent proteins and chemical fluorophores.

Focal plane is a community of microscopists. Membership is free and gives you access to the expertise of mi

Microlist is an extensive, searchable database of microscopy-based resources. Includes data on job listings, protocols, example images, courses, conferences, and more.

RMS Equity in Microscopy Resources. Interactive map of micorscopists from under-represented groups from around the world.


Membership to Micrographia@Western is available to all faculty, students, and staff at Western University and its affiliate colleges and hospitals.

Membership is free!

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