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Imaging Latin America

An All-expenses-paid Microscopy and Image Analysis Workshop
for Latin American Researchers

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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]

Imaging Rotation Groups [PDF]

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End-of-Course Survey

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Job Posting: Advanced Microscopy Imaging Fellow at the Advanced Imaging Center

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Join the conversation on Twitter:

#ImagingLatinAmerica | @AICjanelia@advanced_unit | Twitter List

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DOWNLOADS

Introduction Slide

Please click here to download a slide you will use to introduce yourself to the group. Please stay within the space allotted for each question; you will only have one minute to present your slide to the group. For the image, you may add a microscope image you have acquired or another image that is reflective of your research. Please return your completed slide to imaginglatinamerica@gmail.com by Monday, Sept 12 with the subject line ILA 2022 Introduction Slide.

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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
Click here to download for Windows
Click here to download for Linux

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Sample Images for Fiji Lectures
1.15 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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2022-09-18 Imaging Latin America Group Photo.jpg
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Lecture Notes

Workshop Introduction

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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Introduction to Microscopy I

Image formation, magnification, resolution, objective lenses

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Introduction to Microscopy II

Kohler illumination, microscope configurations, contrast in microscopy

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Fundamentals of Image Processing

Histograms, displays, pixel adjustment, filters, kernels 
 

Fourier Transformation in Image Processing and Optics

Image processing in Fourier space

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Principles of Fluorescence

History of fluorescence, fluorescent proteins and dyes, FRAP

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Fluorescence Microscopy Modalities

Widefield, TIRF, confocal, two-photon, image scanning microscopy

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Object Segmentation

Turning pixel map into discrete objects

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Object-based Co-localization Analysis

Quantifying overlapping objects

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Pixel-based Co-localization and Intensity Analysis

Colocalization coefficients, ratiometric imaging 

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Live Cell Imaging

Environmental control, photon budget, phototoxicity

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Sample Preparation

Fixation, permeabilization, blocking, antibodies, mounting

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Analysis of Biological Movement

Fluorescence recovery rate, particle tracking, motion analysis

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Object Segmentation with Machine Learning

Introduction to machine learning and trainable segmentation models

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Accurate and Sufficient Scientific Reporting

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

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Colocalization Lab Primer

Introduction to Class Challenge 2

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Imaging Across Biological Length Scales with the Emerging Frontiers in Microscopy

Keynote Lecture by Teng-Leong Chew

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Lab and Analysis Sessions

Imaging Lab1: Transmitted Light Microscopy

Kohler illumination, brightfield microscopy, phase contrast, DIC, image formation demonstration

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Imaging Lab 2: Fluorescence Microscopy

Point spread functions, fixed slide imaging, Fourier optics demonstration


Imaging Lab 3: Live Cell Imaging

Live cell imaging of actin and lysosomes


Imaging Lab 4: Importance of Fixatives
Imaging slides prepared with different fixation methods. Download a fixation protocol here.


Class Challenge 1: Hypothesis Formulation

Hypothesis-driven experimental design
 

Class Challenge 2: Imaging Session

Myosin Imaging

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Class Challenge 2: Analysis Session

Co-localization Analysis. Download the Example Data here.


Analysis Lab: Live Cell Imaging
Tracking, FRAP, kymographs. Download the Example Data here.

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Further Reading

LectureNotes
LabSessions
FurtherReading

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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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 

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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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