top of page

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 Schedule [PDF]

Course Instructors [PDF]

Imaging Rotation Groups [PDF]

End of Course Survey

Join the conversation on Twitter:

#CESW2023 | @cesw2023 |  @AICjanelia | @BMCDB


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

Workshop Introduction

Driving principles and goals of the workshop

Fundamentals of Digital Images

Basic concepts of digital images, file format, color scheme

Introduction to Microscopy I

Image formation, magnification, resolution, objective lenses

Introduction to Microscopy II

Kohler illumination, microscope configurations, contrast in microscopy

Principles of Fluorescence

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

Object Segmentation

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

Live Cell Imaging

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


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


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.


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


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.


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

bottom of page