Skip to main content Accessibility help
×
Home
Hostname: page-component-544b6db54f-prt4h Total loading time: 0.23 Render date: 2021-10-16T21:00:13.056Z Has data issue: true Feature Flags: { "shouldUseShareProductTool": true, "shouldUseHypothesis": true, "isUnsiloEnabled": true, "metricsAbstractViews": false, "figures": true, "newCiteModal": false, "newCitedByModal": true, "newEcommerce": true, "newUsageEvents": true }

Visualization of Localization Microscopy Data

Published online by Cambridge University Press:  18 January 2010

David Baddeley
Affiliation:
Department of Physiology, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
Mark B. Cannell
Affiliation:
Department of Physiology, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
Christian Soeller*
Affiliation:
Department of Physiology, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
*
Corresponding author. E-mail: c.soeller@auckland.ac.nz

Abstract

Localization microscopy techniques based on localizing single fluorophore molecules now routinely achieve accuracies better than 30 nm. Unlike conventional optical microscopies, localization microscopy experiments do not generate an image but a list of discrete coordinates of estimated fluorophore positions. Data display and analysis therefore generally require visualization methods that translate the position data into conventional images. Here we investigate the properties of several widely used visualization techniques and show that a commonly used algorithm based on rendering Gaussians may lead to a 1.44-fold loss of resolution. Existing methods typically do not explicitly take sampling considerations into account and thus may produce spurious structures. We present two additional visualization algorithms, an adaptive histogram method based on quad-trees and a Delaunay triangulation based visualization of point data that address some of these deficiencies. The new visualization methods are designed to suppress erroneous detail in poorly sampled image areas but avoid loss of resolution in well-sampled regions. A number of criteria for scoring visualization methods are developed as a guide for choosing among visualization methods and are used to qualitatively compare various algorithms.

Type
Biological Imaging: Techniques Development and Applications
Copyright
Copyright © Microscopy Society of America 2010

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Baddeley, D., Jayasinghe, I.D., Cremer, C., Cannell, M.B. & Soeller, C. (2009). Light-induced dark states of organic fluochromes enable 30 nm resolution imaging in standard media. Biophys J 96, L22L24.CrossRefGoogle ScholarPubMed
Betzig, E., Patterson, G.H., Sougrat, R., Lindwasser, O.W., Olenych, S., Bonifacino, J.S., Davidson, M.W., Lippincott-Schwartz, J. & Hess, H.F. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 16421645.CrossRefGoogle ScholarPubMed
De Berg, M., Cheong, O. & van Kreveld, M. (2008). Computational Geometry: Algorithms and Applications. Berlin, Heidelberg: Springer-Verlag.CrossRefGoogle Scholar
Egner, A., Geisler, C., von Middendorff, C., Bock, H., Wenzel, D., Medda, R., Andresen, M., Stiel, A.C., Jakobs, S., Eggeling, C., Schönle, A. & Hell, S.W. (2007). Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters. Biophys J 93, 32853290.CrossRefGoogle ScholarPubMed
Finkel, R. & Bentley, J. (1974). Quad trees a data structure for retrieval on composite keys. Acta Informatica 4, 19.CrossRefGoogle Scholar
Fölling, J., Bossi, M., Bock, H., Medda, R., Wurm, C., Hein, B., Jakobs, S., Eggeling, C. & Hell, S. (2008). Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat Methods 5, 943945.CrossRefGoogle ScholarPubMed
Heilemann, M., van de Linde, S., Schüttpelz, M., Kasper, R., Seefeldt, B., Mukher-jee, A., Tinnefeld, P. & Sauer, M. (2008). Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed 47, 61726176.CrossRefGoogle ScholarPubMed
Heintzmann, R. & Sheppard, C. (2007). The sampling limit in fluorescence microscopy. Micron 38, 145149.CrossRefGoogle ScholarPubMed
Hess, S.T., Girirajan, T.P.K. & Mason, M.D. (2006). Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91, 42584272.CrossRefGoogle ScholarPubMed
Rust, M.J., Bates, M. & Zhuang, X. (2006). Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (storm). Nat Methods 3, 793795.CrossRefGoogle Scholar
Shannon, C. (1949). Communication in the presence of noise. Proc IRE 37, 1021.CrossRefGoogle Scholar
Shroff, H., Galbraith, C.G., Galbraith, J.A. & Betzig, E. (2008). Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat Methods 5, 417423.CrossRefGoogle ScholarPubMed
Thompson, R.E., Larson, D.R. & Webb, W.W. (2002). Precise nanometer localization analysis for individual fluorescent probes. Biophys J 82, 2775–83.CrossRefGoogle ScholarPubMed
van Oijen, A., Köhler, J., Schmidt, J., Müller, M. & Brakenhoff, G. (1998). 3-Dimensional super-resolution by spectrally selective imaging. Chem Phys Lett 292, 183187.CrossRefGoogle Scholar
Supplementary material: PDF

Baddeley supplementary figures

Baddeley supplementary figures

Download Baddeley supplementary figures(PDF)
PDF 360 KB
87
Cited by

Send article to Kindle

To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Visualization of Localization Microscopy Data
Available formats
×

Send article to Dropbox

To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

Visualization of Localization Microscopy Data
Available formats
×

Send article to Google Drive

To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

Visualization of Localization Microscopy Data
Available formats
×
×

Reply to: Submit a response

Please enter your response.

Your details

Please enter a valid email address.

Conflicting interests

Do you have any conflicting interests? *