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.
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To keep in touch with everyone in the future:
Directory of Course Participants and Instructors: Access it here!
Course WhatsApp Group: Join here!
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Jump to: Lecture Notes | Labs and Analysis Sections | Further Reading
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COURSE INFORMATION
Course Schedule [PDF]
Course Instructors [PDF]
Join the conversation on Twitter:
#OKAscope | @AICjanelia | @OISTedu | Twitter List
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DOWNLOADS
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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
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Sample Images for Fiji Lectures
0.9 GB of images [download .zip].
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PHOTOS
If you would like to share photos of the course, you may add them to this Google Drive folder.
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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!)
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"It is the sample.
Garbage in means garbage out.
Fiji doesn't care.
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mCherry, a curse,
Worst of the fluorescent lot,
Haunting your image.
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It always depends.
Every photon is sacred.
There is no free lunch.
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NA's everything.
It's Fourier Transformation.
Physics, not magic."
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--- OMW Teaching Team
[ ChatGPT contributed too -- guess which one ;) ]
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Lecture Notes
Driving principles and goals of the workshop
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Fundamentals of Digital Images
Basic concepts of digital images, file format, color scheme
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Image formation, magnification, resolution, objective lenses
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Kohler illumination, microscope configurations, contrast in microscopy
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Histograms, displays, pixel adjustment, filters, kernels
Histograms, displays, pixel adjustment, filters, kernels
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FIJI: Fourier Transformation in Image Processing
Image processing in Fourier space
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Fluorescence Microscopy Modalities
Widefield, TIRF, confocal, two-photon, image scanning microscopy
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Turning pixel map into discrete objects
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FIJI: Object Segmentation with Machine Learning
Introduction to machine learning and trainable segmentation models
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SIM, Airyscan, STED and SMLM
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FIJI: Object-based Colocalization
Quantifying overlapping objects
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FIJI: Pixel-based Colocalization and Intensity Analysis
Colocalization coefficients, ratiometric imaging
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Advanced Fluorescence Techniques
FRET, FRAP, FLIP, photomanipulation
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Environmental control, photon budget, phototoxicity
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FIJI: Measurement of Dynamic Changes
Fluorescence recovery rate, particle tracking, motion analysis
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Open-source ML techniques for improving SNR, deblurring, etc.
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The effects of inaccurate and insufficient documentation, and what constitutes good scientific reporting
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Exploring the Potential of Image Analysis & AI for Automated Microscopy Workflows
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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
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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
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Introduction to Analysis Lab II
Analysis Lab II: Colocalization
Colocalization Analysis
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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
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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
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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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Aaron J., Chew TL. (2018) Analysis of Image Similarity and Relationship. In: Jerome W., Price R. (eds) Basic Confocal Microscopy. Springer, Cham (PDF)
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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
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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
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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
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Accuracy and precision in quantitative fluorescence microscopy
Jennifer C. Waters
J. Cell Biol. 2009 187: 1135-1148
doi: 10.1083/jcb.200903097
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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
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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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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
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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
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A list of useful microscopy resources can be found at:
https://www.janelia.org/support-team/integrative-imaging/additional-information
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Jump to: Top | Lecture Notes | Lab and Analysis Sections | Further Reading
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