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