California's Emerging Scientist
Imaging Workshop
An All-expenses-paid Microscopy and Image Analysis Workshop
Jump to: Lecture Notes | Labs and Analysis Sections | Further Reading
​
COURSE INFORMATION
Course Schedule [PDF]
Course Instructors [PDF]
Imaging Rotation Groups [PDF]
​
​
Join the conversation on Twitter:
#CESW2023 | @cesw2023 | @AICjanelia | @BMCDB
​
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
Click here to download for Windows
Click here to download for Linux
​
Sample Images for Fiji Lectures
1.15 GB of images [download .zip]
​
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
​
History of fluorescence, fluorescent proteins and dyes, FRAP
​
Fundamentals of Image Processing
Histograms, displays, pixel adjustment, filters, kernels
​
Fluorescence Microscopy Modalities
Widefield, TIRF, confocal, two-photon, image scanning microscopy
​
Turning pixel map into discrete objects
​
Object Segmentation with Machine Learning
Introduction to machine learning and trainable segmentation models
​
Object-based Co-localization Analysis
Quantifying overlapping objects
​
Environmental control, photon budget, phototoxicity
​
Intensity Measurements and Ratiometric Analysis
Measuring fluorescence intensity, relative intensity measurements
​
Analysis of Biological Movement
Kymographs, FRAP analysis, particle tracking
​
Accurate and Sufficient Scientific Reporting
The effects of inaccurate and insufficient documentation, and what constitutes good scientific reporting
​
Imaging Across Biological Length Scales with the Emerging Frontiers in Microscopy
Keynote Lecture by Chad Hobson
Lab and Analysis Sessions
Imaging Lab1: Transmitted Light Microscopy
Kohler illumination, brightfield microscopy, phase contrast, DIC
​
Imaging Lab 2: Fluorescence Microscopy
Point spread functions, fixed slide imaging
Imaging Lab 3: Live Cell Imaging
ERK biosensor translocation, stress granule dynamics, calcium dynamics
Group Project: Analysis Lab
ERK biosensor translocation. Download the example data here (1.06 GB).
​
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
​
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
​
Jump to: Lecture Notes​ | Labs and Analysis Sections | Further Reading
​
​