QFM 2024
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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" on Fiji and select "Open" to run]
Click here to download for Windows
Sample Images for Lectures
0.9 GB of images [download .zip].
Lecture Notes
Fundamentals of Digital Images
Basic concepts of digital images, file format, color scheme
Fundamentals of Image Processing
Histograms, displays, pixel adjustment, filters, kernels
Image processing in Fourier space
Recognizing and understanding bias in analyzing and interpreting data
Turning pixel map into discrete objects
Quantifying overlapping objects
Colocalization coefficients, ratiometric imaging
Analysis of Biological Movement
Fluorescence recovery rate, particle tracking, motion analysis
Machine Learning in Image Analysis
Supervised/Unsupervised learning, decision trees, object segmentation with ML
Open-source ML techniques for improving SNR, deblurring, etc.
Accurate and Sufficient Scientific Reporting
The effects of inaccurate and insufficient documentation, and what constitutes good scientific reporting
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
Analysis of Image Similarity and Relationship
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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