Imaging Africa 2022
An all-expenses-paid microscopy and image analysis workshop for life science researchers in Africa.
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Location: Cape Town, South Africa
Workshop Dates: 21-26 October 2022
Course Information
Please fill out the course evaluation at this link.
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Course Schedule [PDF]
Course Instructors [PDF]
Course Map [PDF]
Imaging Rotation Groups [PDF]
General Information [PDF]: Travel, lodging, code of conduct, and COVID guidelines
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Join the conversation on Twitter:
#ImagingAfrica | @ImagingAfrica | @AICjanelia | Twitter List
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DOWNLOADS
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
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Sample Images
We will use these downloadable sample images [1.15 GB .zip] during the FIJI lectures.
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Photos
You may share photos with others in the course by adding them to this folder.
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Lecture Notes
Driving principles and goals of the workshop
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An introduction to microscopy
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Including an introduction to the Thor labs demo kit
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Digital Images as Quantitative Data Sources
Basic concepts of digital images, file format, color scheme
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Introduction to fluorescent proteins and dyes
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Fixation, permeabilization, blocking, antibodies, mounting
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Fundamentals of Imaging Processing
Histograms, displays, pixel adjustment, filters, kernels
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Fourier Transform in Image Processing and Optics
Image processing in Fourier space
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Fluorescence Microscopy Modalities
Widefield, TIRF, confocal, deconvolution
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Turning pixel maps into discrete objects
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Object Segmentation with Machine Learning
Introduction to machine learning and trainable segmentation models
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Live imaging challenges and considerations, light sheet
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Techniques for super-resolution imaging
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Object-based Co-localization Analysis
Quantifying overlapping objects
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Pixel-based Co-localization and Intensity Analysis
Co-localization coefficients, ratiometric imaging
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Advanced Fluorescence Techniques
FRET, FRAP
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Image restoration with machine learning
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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
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Microscopy Community Initiatives
An introduction to BioImaging North America (BINA)
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Lab and Analysis Sessions
Practical Session 1: Sample Preparation
Fixation techniques and phalloidin staining
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Practical Session 2: Mobile Microscopy
Portable microscopes for use in the field
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Imaging Lab 1: Transmitted and Fluorescence Modalities
Brightfield, epifluorescence, confocal
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Imaging Lab 2: Enhanced Resolution Imaging
SIM, Airyscan, Thunder
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Imaging Lab 3: Live Cell Imaging
Tracking, FRAP
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Class Project 1: Hypothesis Formulation
Hypothesis-driven experimental design
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Class Project 2: Imaging Session
Myosin imaging
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Class Project 2: Analysis Session
Co-localization analysis. If necessary, download example co-localization data here.
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Analysis Lab: Live Cell Imaging
Tracking, FRAP. If necessary, download the live cell imaging example data here.
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
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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
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A guide to accurate reporting in digital image processing – can anyone reproduce your microscopy?
Jesse S. Aaron, Teng-Leong Chew
J Cell Sci. 2021
doi:10.1242/jcs.254151
See also the link to the checklist
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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.
doi:10.1242/jcs.250027
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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
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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
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Imaging methods are vastly underrepresented biomedical research
Guillermo Marques, Thomas Pengo, Mark A. Sanders
eLife. 2020 9:e55133
doi: 10.7554/eLife.55133
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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
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​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
doi:10.1111/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.
doi: https://doi.org/10.1529/biophysj.103.038422
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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
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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
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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
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Fluorescence Microscopy – Avoiding the Pitfalls
Claire M. Brown
J Cell Sci. 2007
doi: 10.1242/jcs.022079
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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
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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
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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
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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
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