Okinawa Microscopy Workshop 2024
An all-expenses-paid Microscopy and Image Analysis Workshop
for life scientists working in Japan and Southeast Asia
This website will be continuously updated leading up to and throughout the workshop.
Please check back (and refresh the page!) regularly for new uploads and links.
To keep in touch with everyone in the future:
Directory of Course Participants and Instructors: Access it here!
Course WhatsApp Group: Join here!
Jump to: Lecture Notes | Labs and Analysis Sections | Further Reading
COURSE INFORMATION
Course Schedule [PDF]
Course Instructors [PDF]
Join the conversation on Twitter:
#OKAscope | @AICjanelia | @OISTedu | Twitter List
DOWNLOADS
Fiji Program
You should use this version even if you already have Fiji installed on your laptop.
Do not update Fiji after installation.
Click here to download for Mac [after download "Ctrl+Click" and select "Open" to run]
Click here to download for Windows
Sample Images for Fiji Lectures
0.9 GB of images [download .zip].
PHOTOS
If you would like to share photos of the course, you may add them to this Google Drive folder.
The cohort from OMW 2024! Look at all these smiling faces! And some words of wisdom...
(To "decode" this image, go to the Photos folder above to download it!)
"It is the sample.
Garbage in means garbage out.
Fiji doesn't care.
mCherry, a curse,
Worst of the fluorescent lot,
Haunting your image.
It always depends.
Every photon is sacred.
There is no free lunch.
NA's everything.
It's Fourier Transformation.
Physics, not magic."
--- OMW Teaching Team
[ ChatGPT contributed too -- guess which one ;) ]
Lecture Notes
Driving principles and goals of the workshop
Fundamentals of Digital Images
Basic concepts of digital images, file format, color scheme
Image formation, magnification, resolution, objective lenses
Kohler illumination, microscope configurations, contrast in microscopy
Histograms, displays, pixel adjustment, filters, kernels
Histograms, displays, pixel adjustment, filters, kernels
FIJI: Fourier Transformation in Image Processing
Image processing in Fourier space
Fluorescence Microscopy Modalities
Widefield, TIRF, confocal, two-photon, image scanning microscopy
Turning pixel map into discrete objects
FIJI: Object Segmentation with Machine Learning
Introduction to machine learning and trainable segmentation models
SIM, Airyscan, STED and SMLM
FIJI: Object-based Colocalization
Quantifying overlapping objects
FIJI: Pixel-based Colocalization and Intensity Analysis
Colocalization coefficients, ratiometric imaging
Advanced Fluorescence Techniques
FRET, FRAP, FLIP, photomanipulation
Environmental control, photon budget, phototoxicity
FIJI: Measurement of Dynamic Changes
Fluorescence recovery rate, particle tracking, motion analysis
Open-source ML techniques for improving SNR, deblurring, etc.
The effects of inaccurate and insufficient documentation, and what constitutes good scientific reporting
Exploring the Potential of Image Analysis & AI for Automated Microscopy Workflows
Lab and Analysis Sessions
Imaging Lab1: Basic Microscopy Techniques
Köhler Illumination, Brightfield Microscopy, Dark Field Microscopy, Phase Contrast Microscopy, Differential Interference Contrast (DIC) Microscopy, Widefield Fluorescence Microscopy
Imaging Lab 2: Advanced Microscopy Techniques
Laser Scanning Confocal Microscopy, Spinning Disk Confocal Microscopy, Light-Sheet Microscopy, Two-Photon Microscopy
Imaging Lab 3: Super-Resolution Techniques
Airyscan, Structured Illumination Microscopy (SIM), Single-Molecule Localization Microscopy (SMLM), Stimulated Emission Depletion (STED) Microscopy
Imaging Lab 4: Live Cell Imaging
Fluorescence Recovery After Photobleaching (FRAP) and Lysosome Tracking
Class Challenge: Hypothesis Formation and Experimental Design
Hypothesis-driven experimental design
Analysis Lab I: Live Cell Imaging
Tracking, FRAP
Introduction to Analysis Lab II
Analysis Lab II: Colocalization
Colocalization Analysis
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
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
Eric C. Wait, Michael A. Reiche, Teng-Leong Chew
J Cell Sci 2020 133.
doi:10.1242/jcs.250027
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
Aaron J., Chew TL. (2018) Analysis of Image Similarity and Relationship. In: Jerome W., Price R. (eds) Basic Confocal Microscopy. Springer, Cham (PDF)
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
doi:10.1111/jmi.12588
Automatic and quantitative measurement of protein-protein colocalization in live cells
Costes, S. V., Daelemans, D., Cho, E. H., Dobbin, Z., Pavlakis, G. and Lockett, S.
Biophys. J 2004 86: 3993-4003.
doi: https://doi.org/10.1529/biophysj.103.038422
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
Phototoxicity in live fluorescence microscopy, and how to avoid it
Jaroslav Icha, Michael Weber, Jennifer C. Waters, and Caren Norden
BioEssays, 2017
doi: 10.1002/bies.201700003
Believing is seeing – the deceptive influence of bias in quantitative microscopy
Rachel M. Lee, Leanna R. Eisenman, Satya Khuon, Jesse S. Aaron, Teng-Leong Chew
J. Cell Sci. 2024
doi: 10.1242/jcs.261567
A list of useful microscopy resources can be found at:
https://www.janelia.org/support-team/integrative-imaging/additional-information
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