Image Acquisition

Basics of digital microscopy. Wallace CT, Jessup M, Bernas T, Pena KA, Calderon MJ, Loughran PA. Current Protocols in Cytometry 2018, 83, 12.2.1–12.2.14. doi: 10.1002/cpcy.31

A biologist's guide to planning and performing quantitative bioimaging experiments. Senft RA, Diaz-Rohrer B, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL 3rd, Eliceiri KW, Cimini BA. PLoS Biol. 2023 Jun 27;21(6):e3002167. doi: 10.1371/journal.pbio.3002167.

Tutorial: guidance for quantitative confocal microscopy. Jonkman J, Brown CM, Wright GD, Anderson KI, NorthAJ. Nature Protocols 2020, 15: 1585–1611. DOI:10.1038/s41596-020-0307-7

Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. North AJ. J Cell Biol 2006, 172(1): 9–18. DOI: 10.1083/jcb.200507103

The 39 Steps: A Cautionary Tale of Quantitative 3-D Fluorescence Microscopy. Pawley J. BioTechniques 2000, 28:884-887. DOI: 10.2144/00285bt01

Fluorescence microscopy – avoiding the pitfalls. Brown CM. J Cell Sci 2007, 120(19): 1703-1705. DOI:10.1242/jcs.03433

Accuracy and precision in quantitative fluorescence microscopy. Waters JC. J Cell Biol 2009, 185(7): 1135–1148. DOI: 10.1083/jcb.200903097

Image Analysis

Believing is seeing - the deceptive influence of bias in quantitative microscopy. Lee RM, Eisenman LR, Khuon S, Aaron JS, Chew TL. J Cell Sci. 2024 Jan 1;137(1):jcs261567. doi: 10.1242/jcs.261567.

Made to measure: An introduction to quantifying microscopy data in the life sciences. Culley S, Caballero AC, Burden JJ, Uhlmann V. J Microsc. 2023 Jun 2. doi: 10.1111/jmi.13208.

Interpreting Fluorescence Microscopy Images and Measurements. Waters JC. and Swedlow J.R., 2007 in Evaluating Techniques in Biochemical Research, D. Zuk, ed. (Cambridge, MA: Cell Press).

Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Cromey DW. Sci Eng Ethics 2010;16(4):639-667. DOI:10.1007/s11948-010-9201-y

What’s in a picture? The temptation of image manipulation. Rossner M and Yamada KM. J Cell Biol 2004 Jul 5;166(1):11-15. DOI: 10.1083/jcb.200406019.

A Pixel Is Not A Little Square, A Pixel Is Not A Little Square, A Pixel Is Not A Little Square, (And a Voxel is Not a Little Cube). Alvy RaySmith. Microsoft Tech Memo 6, July 17 1995

A simple method for quantitating confocal fluorescent images. Shihan MH , Novo SG , Le Marchand SJ , Wang Y, Duncan MK. Biochem Biophys Rep 2021 Feb 1:25:100916. doi: 10.1016/j.bbrep.2021.100916.

What to use to express the variability of data: Standard deviation or standard error of mean? Barde MP, Barde PJ. Perspect Clin Res 2012 Jul;3(3):113-6. doi: 10.4103/2229-3485.100662

Quantitating the cell: turning images into numbers with ImageJ. Arena ET, Rueden CT, Hiner MC, Wang S,Yuan M, Eliceiri KW. Wiley Interdiscip Rev Dev Biol. 2017;6(2). doi: 10.1002/wdev.260

Basic image analysis and manipulation in ImageJ/Fiji. Stossi F, Singh PK, Current Protocols 2023,3, e849.2023. doi: 10.1002/cpz1.849

Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Cimini BA, J Microsc. 2024; 295(2):93-101. doi: 10.1111/jmi.13288

From Image to Data Using Common Image-Processing Techniques. Sysko LR, Davis MA. Curr. Protoc. Cytom. 2010, 54:12.21.1-12.21.17, doi: 10.1002/0471142956.cy1221s54

Live-Cell Imaging

Phototoxicity in live fluorescence microscopy, and how to avoid it. Icha J, Weber M, Waters JC, Norden C. Bioessays 2017 Aug;39(8). DOI: 10.1002/bies.201700003.

Optimizing live-cell fluorescence imaging conditions to minimize phototoxicity. Kiepas A, Voorand E, Mubaid F, Siegel PM, Brown CM. J Cell Sci. 2020 Feb 21;133(4):jcs242834. doi: 10.1242/jcs.242834.

Optimizing Long-Term Live Cell Imaging. Lac A, Le Lam A, Heit B. Methods Mol Biol. 2022;2440:57-73. doi: 10.1007/978-1-0716-2051-9_3.

Circumventing photodamage in live-cell microscopy. Magidson V, Khodjakov A. Methods Cell Biol. 2013 ; 114: . doi: 10.1016/B978-0-12-407761-4.00023-3

Live-cell imaging. Cole R. Cell Adhesion & Migration 2014, 8:5, 452-459, doi:10.4161/cam.28348

Publishing Images

A guide to accurate reporting in digital image acquisition – can anyone replicate your microscopy data? Heddleston JM, Aaron JS, Khuon S Chew T-L. J Cell Sci 2021, 134 (6): jcs254144. DOI:10.1242/jcs.254144

A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis? Aaron J, Chew TL. J Cell Sci 2021, 134(6):jcs254151. DOI: 10.1242/jcs.254151

Best practices and tools for reporting reproducible fluorescence microscopy methods. Montero LP, Senft RA, Ross-Elliott TJ et al. Nat Methods 2021;18: 1463–1476. DOI: 10.1038/s41592-021-01156-w

Reproducible image handling and analysis. Miura K, Nørrelykke SF. EMBO J. 2021 Feb 1;40(3):e105889. doi: 10.15252/embj.2020105889.