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Imaging Africa 2022

An all-expenses-paid microscopy and image analysis workshop for life science researchers in Africa.

Location: Cape Town, South Africa

Workshop Dates: 21-26 October 2022

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Course Information

Please fill out the course evaluation at this link.

Course Schedule [PDF]

Course Instructors [PDF]

Course Map [PDF]

Imaging Rotation Groups [PDF]

General Information [PDF]: Travel, lodging, code of conduct, and COVID guidelines

Join the conversation on Twitter:

#ImagingAfrica | @ImagingAfrica | @AICjanelia | Twitter List


FIJI Program

You should use this version even if you already have FIIJI installed on your laptop.

Do NOT update FIJI after installation.

Click here to download for Mac

Click here to download for Windows

Click here to download for Linux

Sample Images

We will use these downloadable sample images [1.15 GB .zip] during the FIJI lectures.


You may share photos with others in the course by adding them to this folder.


Lecture Notes

Workshop Introduction

Driving principles and goals of the workshop

Introduction to Optics I

An introduction to microscopy

Introduction to Optics II

Including an introduction to the Thor labs demo kit

Digital Images as Quantitative Data Sources

Basic concepts of digital images, file format, color scheme

Basics of Fluorescence

Introduction to fluorescent proteins and dyes

Sample Preparation

Fixation, permeabilization, blocking, antibodies, mounting

Fundamentals of Imaging Processing

Histograms, displays, pixel adjustment, filters, kernels

Fourier Transform in Image Processing and Optics

Image processing in Fourier space

Fluorescence Microscopy Modalities

Widefield, TIRF, confocal, deconvolution

Object Segmentation

Turning pixel maps into discrete objects

Object Segmentation with Machine Learning

Introduction to machine learning and trainable segmentation models

Live Cell Imaging

Live imaging challenges and considerations, light sheet

Super-resolution Microscopy

Techniques for super-resolution imaging

Object-based Co-localization Analysis

Quantifying overlapping objects

Pixel-based Co-localization and Intensity Analysis

Co-localization coefficients, ratiometric imaging

Advanced Fluorescence Techniques


Open-Source Gems

Image restoration with machine learning

Accurate and Sufficient Scientific Reporting

The effects of inaccurate and insufficient documentation and what constitutes good scientific reporting


Analysis of Biological Movement

Kymographs, FRAP, Particle Tracking

Microscopy Community Initiatives

An introduction to BioImaging North America (BINA)

Lecture Notes

Lab and Analysis Sessions

Lab and Analysis Sessons

Further Reading

When Light Meets Biology: How the Specimen Affects Quantitative Microscopy
Michael Reiche, Jesse Aaron, Ulrike Böhm, Michael DeSantis, Chad Hobson, Satya Khuon, Rachel Lee, and Teng-Leong Chew
J. Cell Sci. 2022
doi: 10.1242/jcs.259656

A guide to accurate reporting in digital image acquisition – can anyone replicate your microscopy?
John M. Heddleston, Jesse S. Aaron, Satya Khuon, Teng-Leong Chew
J Cell Sci. 2021
doi: 10.1242/jcs.254144

See also the link to the checklist

A guide to accurate reporting in digital image processing – can anyone reproduce your microscopy?
Jesse S. Aaron, Teng-Leong Chew
J Cell Sci. 2021

See also the link to the checklist

Hypothesis-driven quantitative fluorescence microscopy – the importance of reverse-thinking in experimental design
Eric C. Wait, Michael A. Reiche, Teng-Leong Chew
J Cell Sci. 2020 133.

Practical considerations in particle and object tracking and analysis
Jesse S. Aaron, Eric Wait, Michael DeSantis, Teng-Leong Chew
Curr Prot Cell Biol. 2019 e88.
doi: 10.1002/cpcb.88

Image co-localization – co-occurrence versus correlation
Jesse S. Aaron, Aaron B. Taylor, Teng-Leong Chew
J Cell Sci. 2018 131: jcs211847
doi: 10.1242/jcs.211847

Imaging methods are vastly underrepresented biomedical research
Guillermo Marques, Thomas Pengo, Mark A. Sanders
eLife. 2020 9:e55133
doi: 10.7554/eLife.55133

Model-free quantification and visualization of colocalization in fluorescence images
Aaron B. Taylor, Maria S. Ioannou, Jesse S. Aaron, Teng-Leong Chew
Cytometry Part A. 2018 
doi: 10.1002/cyto.a.23356

​Perceptually accurate display of two greyscale images as a single colour image
Aaron.B. Taylor, Maria.S. Ioannou, Takashi Watanabe, Klaus Hahn, Teng-Leong Chew
J. Microscopy. 2018 268: jmi.12588


​Automatic and quantitative measurement of protein-protein colocalization in live cells
S. V. Costes, D. Daelemans, E. H. Cho, Z. Dobbin, G. Pavlakis, and S. Lockett
Biophys. J 2004 86: 3993-4003.

Seeing is believing? A beginners' guide to practical pitfalls in image acquisition
Alison J. North
J. Cell Biol. 2006 172: 9-18
doi: 10.1083/jcb.200507103


Accuracy and precision in quantitative fluorescence microscopy
Jennifer C. Waters
J. Cell Biol. 2009 187: 1135-1148
doi: 10.1083/jcb.200903097


Protein-Retention Expansion Microscopy (ExM): Scalable and Convenient Super-Resolution Microscopy
Paul Tillberg
Methods Mol Biol. 2021 2304:147-156.
doi: 10.1007/978-1-0716-1402-0_7


​What If Scientists Shared Their Reagents for Free?
Amanda Heidt
The Scientist. July 2022 Issue 2

Transfection of Cultured Primary Neurons
Annalisa Rossi, Ralf Dahm, and Paolo Macchi
Stem Cell Technologies in Neuroscience. 2017
doi: 10.1007/978-1-4939-7024-7_4

Analysis of Image Similarity and Relationship

Jesse Aaron and Teng-Leong Chew

Basic Confocal Microscopy. 2018 309-333

doi: 10.1007/978-3-319-97454-5_11

Fluorescence Microscopy – Avoiding the Pitfalls

Claire M. Brown

J Cell Sci. 2007

doi: 10.1242/jcs.022079

Tutorial: Guidance for Quantitative Confocal Microscopy

James Jonkman, Claire M. Brown, Graham D. Wright, Kurt I. Anderson, and Alison J. North

Nature Protocols. 2020 15:1585-1611

doi: 10.1038/s41596-020-0313-9

Designing a rigorous microscopy experiment: Validating methods and avoiding bias

Anna Payne-Tobin Jost and Jennifer C. Waters

J. Cell Bio. 2019 218(5):1452-1466

doi: 10.1083/jcb.201812109

A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments

Jen-Yi Lee and Maiko Kitaoka

MBoC. 2018 29:1519-1525

doi: 10.1091/mbc.E17-05-0276

Concepts in quantitative fluorescence microscopy

Jennnifer C. Waters and Torsten Wittmann

Methods in Cell Biology. 2014 123:1-18

doi: 10.1016/B978-0-12-420138-5.00001-X

Futher Reading
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