Our favorites

Arganda-Carreras, Ignacio, Verena Kaynig, Curtis Rueden, Kevin W. Eliceiri, Johannes Schindelin, Albert Cardona, and H. Sebastian Seung. 2017. “Trainable Weka Segmentation: A Machine Learning Tool for Microscopy Pixel Classification.” Bioinformatics  33 (15): 2424–26.

Axelrod, D. 2001. “Total Internal Reflection Fluorescence Microscopy in Cell Biology.” Traffic  2 (11): 764–74.

Bancaud, Aurélien, Sébastien Huet, Gwénaël Rabut, and Jan Ellenberg. 2010. “Fluorescence Perturbation Techniques to Study Mobility and Molecular Dynamics of Proteins in Live Cells: FRAP, Photoactivation, Photoconversion, and FLIP.” Cold Spring Harbor Protocols 2010 (12): db. top90.

Banterle, N. et al. (2013) Fourier ring correlation as a resolution criterion for super-resolution microscopy. J. Struct. Biol.183, 363–367

Bolte, S., and F. P. Cordelières. 2006. “A Guided Tour into Subcellular Colocalization Analysis in Light Microscopy.” Journal of Microscopy 224 (Pt 3): 213–32.

Burgert, Anne, Sebastian Letschert, Sören Doose, and Markus Sauer. 2015. “Artifacts in Single-Molecule Localization Microscopy.” Histochemistry and Cell Biology 144 (2): 123–31.

Burry, Richard W. 2011. “Controls for Immunocytochemistry: An Update.” The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society 59 (1): 6–12.

Caicedo, Juan C., Sam Cooper, Florian Heigwer, Scott Warchal, Peng Qiu, Csaba Molnar, Aliaksei S. Vasilevich, et al. 2017. “Data-Analysis Strategies for Image-Based Cell Profiling.” Nature Methods 14 (9): 849–63.

Conchello, José-Angel, and Jeff W. Lichtman. 2005. “Optical Sectioning Microscopy.” Nature Methods 2 (12): 920–31.

Costantini, Lindsey M., Mikhail Baloban, Michele L. Markwardt, Mark Rizzo, Feng Guo, Vladislav V. Verkhusha, and Erik L. Snapp. 2015. “A Palette of Fluorescent Proteins Optimized for Diverse Cellular Environments.” Nature Communications 6 (July): 7670.

Costantini, Lindsey M., Matteo Fossati, Maura Francolini, and Erik Lee Snapp. 2012. “Assessing the Tendency of Fluorescent Proteins to Oligomerize Under Physiologic Conditions.” Traffic  13 (5): 643–49.

Couchman, John R. 2009. “Commercial Antibodies: The Good, Bad, and Really Ugly.” The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society 57 (1): 7–8.

Cox, G. and Sheppard, C.J.R. (2004) Practical limits of resolution in confocal and non-linear microscopy. Microsc. Res. Tech. 63, 18–22

Dempsey, G.T. et al. (2011) Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat. Methods 8, 1027–1036

Dunsby, C. (2008) Optically sectioned imaging by oblique plane microscopy. Opt. Express 16, 20306–20316

Eliceiri, Kevin W., Michael R. Berthold, Ilya G. Goldberg, Luis Ibáñez, B. S. Manjunath, Maryann E. Martone, Robert F. Murphy, et al. 2012. “Biological Imaging Software Tools.” Nature Methods 9 (7): 697–710.

Engelbrecht, C.J. and Stelzer, E.H. (2006) Resolution enhancement in a light-sheet-based microscope (SPIM). Opt. Lett.31, 1477–1479

Fischer, R. S., Y. Wu, P. Kanchanawong, and H. Shroff. 2011. “Microscopy in 3D: A Biologist’s Toolbox.” Trends in Cell …, January. http://www.sciencedirect.com/science/article/pii/S096289241100198X.

Garcia-Fossa, F. et al. (2023) Interpreting image-based profiles using similarity clustering and single-cell visualization. Curr. Protoc. 3, e713

Goodwin, Paul C. 2013. “Chapter 15 – Evaluating Optical Aberrations Using Fluorescent Microspheres: Methods, Analysis, and Corrective Actions.” In Methods in Cell Biology, edited by Greenfield Sluder and David E. Wolf, 114:369–85. Academic Press.

Grünwald, David, Shailesh M. Shenoy, Sean Burke, and Robert H. Singer. 2008. “Calibrating Excitation Light Fluxes for Quantitative Light Microscopy in Cell Biology.” Nature Protocols 3 (11): 1809–14.

Hell, S.W. (2003) Toward fluorescence nanoscopy. Nat. Biotechnol. 21, 1347–1355

Hell, S. et al. (2011) Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index. J. Microsc. 169, 391–405

Hiraoka, Y., J. W. Sedat, and D. A. Agard. 1990. “Determination of Three-Dimensional Imaging Properties of a Light Microscope System. Partial Confocal Behavior in Epifluorescence Microscopy.” Biophysical Journal 57 (2): 325–33.

Hobson, C.M. et al. (2022) Practical considerations for quantitative light sheet fluorescence microscopy. Nat. Methods 19, 1538–1549

Hofmann, M. et al. (2005) Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proceedings of the National Academy of Sciences 102, 17565–17569

Holman, Luke, Megan L. Head, Robert Lanfear, and Michael D. Jennions. 2015. “Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording.” PLoS Biology 13 (7): e1002190.

Huang, F. et al. (2013) Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms. Nat. Methods 10, 653–658

Huisken, Jan, Jim Swoger, Filippo Del Bene, Joachim Wittbrodt, and Ernst H. K. Stelzer. 2004. “Optical Sectioning Deep inside Live Embryos by Selective Plane Illumination Microscopy.” Science 305 (5686): 1007–9.

Jambor, H. et al. (2021) Creating clear and informative image-based figures for scientific publications. PLoS Biol. 19, e3001161

Jost, Anna Payne-Tobin, and Jennifer C. Waters. 2019. “Designing a Rigorous Microscopy Experiment: Validating Methods and Avoiding Bias.” The Journal of Cell Biology, March. https://doi.org/10.1083/jcb.201812109.

Kan, Andrey. 2017. “Machine Learning Applications in Cell Image Analysis.” Immunology and Cell Biology 95 (6): 525–30.

Keller, H. Ernst. 2007. “Proper Alignment of the Microscope.” Methods in Cell Biology 81 (January): 43–53.

Krzywinski, Martin, and Naomi Altman. 2013. “Points of Significance: Error Bars.” Nature Methods 10 (10): 921–22.

Kwon, Jiwoong, Jihee Hwang, Jaewan Park, Gi Rim Han, Kyu Young Han, and Seong Keun Kim. 2015. “RESOLFT Nanoscopy with Photoswitchable Organic Fluorophores.” Scientific Reports 5 (December): 17804.

Laissue, P. Philippe, Rana A. Alghamdi, Pavel Tomancak, Emmanuel G. Reynaud, and Hari Shroff. 2017. “Assessing Phototoxicity in Live Fluorescence Imaging.” Nature Methods 14 (7): 657–61.

Lambert, Talley J., and Jennifer C. Waters. 2016. “Navigating Challenges in the Application of Superresolution Microscopy.” The Journal of Cell Biology 216 (1): 53–63.

Lambert, T.J. and Waters, J.C. (2014) Assessing camera performance for quantitative microscopy. Methods Cell Biol. 123, 35–53 [note, photon transfer curve protocol works for CCD cameras, not sCMOS]

Lichtman, Jeff W., and José-Angel Conchello. 2005. “Fluorescence Microscopy.” Nature Methods 2 (12): 910–19.

Liu, Z. et al. (2015) Imaging live-cell dynamics and structure at the single-molecule level. Mol. Cell 58, 644–659

Lucas, A.M. et al. (2021) Open-source deep-learning software for bioimage segmentation. Mol. Biol. Cell 32, 823–829

Lukinavičius, G. et al. (2014) Fluorogenic probes for live-cell imaging of the cytoskeleton. Nat. Methods 11, 731–733

MacCoun, Robert, and Saul Perlmutter. 2015. “Blind Analysis: Hide Results to Seek the Truth.” Nature 526 (7572): 187–89.

Miura, K. and Nørrelykke, S.F. (2021) Reproducible image handling and analysis. EMBO J. 40, e105889

Model, M. A., and J. K. Burkhardt. 2001. “A Standard for Calibration and Shading Correction of a Fluorescence Microscope.” Cytometry 44 (4): 309–16.

Model, Michael. 2014. “Intensity Calibration and Flat-Field Correction for Fluorescence Microscopes.” Current Protocols in Cytometry / Editorial Board, J. Paul Robinson, Managing Editor… [et Al.] 68 (April): 10.14.1–10.

Murray, John M. 2013. “Practical Aspects of Quantitative Confocal Microscopy.” Methods in Cell Biology 114 (January): 427–40.

Murray, John M., Paul L. Appleton, Jason R. Swedlow, and Jennifer C. Waters. 2007. “Evaluating Performance in Three-Dimensional Fluorescence Microscopy.” Journal of Microscopy 228 (Pt 3): 390–405.

Olivier, Nicolas, Debora Keller, Pierre Gönczy, and Suliana Manley. 2013. “Resolution Doubling in 3D-STORM Imaging through Improved Buffers.” PloS One 8 (7): e69004.

Peng, T. et al. (2017) A BaSiC tool for background and shading correction of optical microscopy images. Nat. Commun.8, 14836

Pete Bankhead, “Introduction · Analyzing Fluorescence Microscopy Images with ImageJ.” 2019. https://petebankhead.gitbooks.io/imagej-intro/content/.

Point by Point: An Introductory Guide to Sample Preparation for Single-Molecule, Super-Resolution Fluorescence Microscopy. 2009. Sample Preparation for Single-Molecule Super-Resolution Fluorescence Microscopy. Hoboken, NJ, USA: John Wiley & Sons, Inc.

Rueden, C.T. et al. (2019) Scientific Community Image Forum: A discussion forum for scientific image software. PLoS Biol. 17, e3000340

Royer, Loic A., Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, and Eugene W. Myers. 2015. “ClearVolume: Open-Source Live 3D Visualization for Light-Sheet Microscopy.” Nature Methods 12 (6): 480–81.

Sage, D. et al. (2015) Quantitative evaluation of software packages for single-molecule localization microscopy. Nat. Methods 12, 717–724

Sage, Daniel, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, et al. 2019. “Super-Resolution Fight Club: Assessment of 2D and 3D Single-Molecule Localization Microscopy Software.” Nature Methods, April. https://doi.org/10.1038/s41592-019-0364-4.

Salmon, E. D., and J. C. Canman. 2001. “Proper Alignment and Adjustment of the Light Microscope.” Current Protocols in Cell Biology / Editorial Board, Juan S. Bonifacino… [et Al.] Chapter 4 (May): Unit 4.1–Uni1.

Sapoznik, E. et al. (2020) A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. Elife 9,

Schermelleh, Lothar, Rainer Heintzmann, and Heinrich Leonhardt. 2010. “A Guide to Super-Resolution Fluorescence Microscopy.” The Journal of Cell Biology 190 (2): 165–75.

Schermelleh, L. et al. (2019) Super-resolution microscopy demystified. Nat. Cell Biol. 21, 72–84

Schindelin, Johannes, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, et al. 2012. “Fiji: An Open-Source Platform for Biological-Image Analysis.” Nature Methods 9 (7): 676–82.

Schmied, C. et al. (2023) Community-developed checklists for publishing images and image analysis. ArXiv DOI: 10.1242/jcs.254151

Schnell, Ulrike, Freark Dijk, Klaas A. Sjollema, and Ben N. G. Giepmans. 2012. “Immunolabeling Artifacts and the Need for Live-Cell Imaging.” Nature Methods 9 (2): 152–58.

Schnitzbauer, Joerg, Maximilian T. Strauss, Thomas Schlichthaerle, Florian Schueder, and Ralf Jungmann. 2017. “Super-Resolution Microscopy with DNA-PAINT.” Nature Protocols 12 (6): 1198–1228.

Sheppard, C.J.R. et al. (1992) Signal-to-noise ratio in confocal microscope systems. J. Microsc. 168, 209–218

Sheppard, C.J.R. and To¨ro¨k, P. (1997) Effects of specimen refractive index on confocal imaging. J. Microsc. 185, 366–374

Shtengel, G. et al. (2009) Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc. Natl. Acad. Sci. U. S. A. 106, 3125–3130

Smith, K. et al. (2015) CIDRE: an illumination-correction method for optical microscopy. Nat. Methods 12, 404–406

Senft, RA, Barbara Diaz-Rohrer,  et al.  A biologist’s guide to the field of quantitative bioimaging. April 2023. https://zenodo.org/record/7439284#.ZELSqezMJhY

Stirling, D.R. et al. (2021) CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics 22, 433

Stirling, D.R. et al. (2021) CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis. Bioinformatics 37, 3992–3994

Sommer, C., C. Straehle, U. Köthe, and F. A. Hamprecht. 2011. “Ilastik: Interactive Learning and Segmentation Toolkit.” In 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 230–33.

Spiering, Désirée, Jose Javier Bravo-Cordero, Yasmin Moshfegh, Veronika Miskolci, and Louis Hodgson. 2013. “Quantitative Ratiometric Imaging of FRET-Biosensors in Living Cells.” Methods in Cell Biology 114 (January): 593–609.

Stelzer, E. H. K. 1998. “Contrast, Resolution, Pixelation, Dynamic Range and Signal-to-Noise Ratio: Fundamental Limits to Resolution in Fluorescence Light Microscopy.” Journal of Microscopy 189 (1): 15–24.

Swedlow, Jason R., Ke Hu, Paul D. Andrews, David S. Roos, and John M. Murray. 2002. “Measuring Tubulin Content in Toxoplasma Gondii: A Comparison of Laser-Scanning Confocal and Wide-Field Fluorescence Microscopy.” Proceedings of the National Academy of Sciences 99 (4): 2014–19.

Tinevez, Jean-Yves, Nick Perry, Johannes Schindelin, Genevieve M. Hoopes, Gregory D. Reynolds, Emmanuel Laplantine, Sebastian Y. Bednarek, Spencer L. Shorte, and Kevin W. Eliceiri. 2017. “TrackMate: An Open and Extensible Platform for Single-Particle Tracking.” Methods  115 (February): 80–90.

Uhlen, Mathias, Anita Bandrowski, Steven Carr, Aled Edwards, Jan Ellenberg, Emma Lundberg, David L. Rimm, et al. 2016. “A Proposal for Validation of Antibodies.” Nature Methods 13 (10): 823–27.

Ulman, Vladimír, Martin Maška, Klas E. G. Magnusson, Olaf Ronneberger, Carsten Haubold, Nathalie Harder, Pavel Matula, et al. 2017. “An Objective Comparison of Cell-Tracking Algorithms.” Nature Methods 14 (12): 1141–52.

Viana, M.P. et al. (2023) Integrated intracellular organization and its variations in human iPS cells. Nature 613, 345–354

van de Linde, S. et al. (2011) Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging. Photochem. Photobiol. Sci. 10, 499–506

Waters, Jennifer C. 2009. “Accuracy and Precision in Quantitative Fluorescence Microscopy.” The Journal of Cell Biology 185 (7): 1135–48.

Weber, Michael, Michaela Mickoleit, and Jan Huisken. 2014. “Light Sheet Microscopy.” Methods in Cell Biology 123 (January): 193–215.

Weigert, Martin, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, et al. 2018. “Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy.” Nature Methods 15 (12): 1090–97.

Wu, Yicong, and Hari Shroff. 2018. “Faster, Sharper, and Deeper: Structured Illumination Microscopy for Biological Imaging.” Nature Methods 15 (12): 1011–19.

Wu, Yicong, Peter Wawrzusin, Justin Senseney, Robert S. Fischer, Ryan Christensen, Anthony Santella, Andrew G. York, et al. 2013. “Spatially Isotropic Four-Dimensional Imaging with Dual-View Plane Illumination Microscopy.” Nature Biotechnology, October. http://www.nature.com/doifinder/10.1038/nbt.2713.

York, A.G. et al. (2013) Instant super-resolution imaging in live cells and embryos via analog image processing. Nat. Methods at <http://www.nature.com/doifinder/10.1038/nmeth.2687>