Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

With the widespread uptake of two-dimensional (2D) and three-dimensional (3D) single-molecule localization microscopy (SMLM), a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effort, we designed a competition to extensively characterize and rank the performance of 2D and 3D SMLM software packages. We generated realistic simulated datasets for popular imaging modalities-2D, astigmatic 3D, biplane 3D and double-helix 3D-and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D SMLM software and provides a holistic view of how the latest 2D and 3D SMLM packages perform in realistic conditions. This resource allows researchers to identify optimal analytical software for their experiments, allows 3D SMLM software developers to benchmark new software against the current state of the art, and provides insight into the current limits of the field.

À propos de ce résultat

Cette page est générée automatiquement et peut contenir des informations qui ne sont pas correctes, complètes, à jour ou pertinentes par rapport à votre recherche. Il en va de même pour toutes les autres pages de ce site. Veillez à vérifier les informations auprès des sources officielles de l'EPFL.

Concepts associés

Chargement

Publications associées

Chargement

Anurag Agrawal, Anna Archetti, Silvia Colabrese, Ricardo Henriques, Seamus John Holden, Tomas Lukes, Thomas Pengo, Thanh-An Michel Pham, Daniel Sage, Michaël Unser
2019
Article

Résumé

Official source

https://infoscience.epfl.ch/record/267336?ln=fr

À propos de ce résultat

Concepts associés (12)

Concepts associés

Chargement

Publications associées (7)

Chargement

Afficher plus

Publications associées

Chargement

Logiciel

thumb|Démarche de construction d'un logiciel. En informatique, un logiciel est un ensemble de séquences d’instructions interprétables par une machine et d’un jeu de données nécessaires à ces opératio

Donnée

Une donnée est ce qui est connu et qui sert de point de départ à un raisonnement ayant pour objet la détermination d'une solution à un problème en relation avec cette donnée. Cela peut être une descr

Nucleic acid double helix

In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as

Development of an interactive genome browser to visualize and analyse large scale genomic data

Lucas Sinclair

Genomic bioinformatics is a growing and developing field. Indeed, data analysis is becoming an integrative and essential part of any quantitative biological experiment as the technologies evolve and the wet lab methods used generate larger and larger quantities of data. Yet few standards have emerged and a plethora of analytical tools exist, none of which are established as a standard. The difficulties arise early on, even before processing any genomic data, as one first needs to visualize it. Several visualization methods exist, such as the UCSC genome browser, IGB or Argo, but none offer a satisfying interface or set of tools. Stemming from a pre-existing project at the bioinformatics and biostatistics core facility, this study presents a new solution to the multiple difficulties that at present beleaguer the field. A novel genome visualization tool is proposed where the user interface remains simple and incorporates a set of common statistical analysis functions. The software produced, entitled gFeatMiner, is capable of processing large scale genomic datasets for computing descriptive statistics and manipulate them in several ways. The program makes use of modern technologies and infrastructure paving the way for its development into an advanced data mining tool. In the second part of this study, a practical application is worked out. Examining the genes coding for ribosomal proteins in the model organism yeast (Saccharomyces cerevisiae) and using several available sets of data including multiple transcription factor binding profiles in vivo and in vitro, RNA polymerase activity and nucleosome enrichment, we attempt to better understand and reveal cellular mechanisms by clustering the numerous genes together using different criteria and machine learning strategies

2010

Chargement

A Psf-Based Approach To Biplane Calibration In 3D Super-Resolution Microscopy

Hagay Kirshner, Suliana Manley, Thomas Pengo, Daniel Sage, Michaël Unser

Super-resolution localization microscopy methods such as PALM and STORM have been shown to provide imaging with resolutions up to a few tens of nanometers while using relatively simple setups. Biplane PALM has extended the PALM technique to three-dimensions, by simultaneously using two imaging planes, with different focal depths. A key aspect in achieving good axial localization results is the alignment of the two planes. Currently available approaches assume that misaligned planes only result in scaling and rotation of the PSF pattern. We show in this work that this does not necessarily hold true, especially in the presence of refractive index mismatch between the different optical layers. Instead, we suggest a calibration algorithm that relies on a realistic PSF model and finds the affine transform that relates the two planes with respect to a point source in the object domain. Our calibration algorithm also determines the defocus distance between the planes.

Ieee2012

Chargement

3D high-density localization microscopy using hybrid astigmatic/biplane imaging and sparse image reconstruction

Lina Carlini, Seamus John Holden, Suliana Manley, Michaël Unser

Localization microscopy achieves nanoscale spatial resolution by iterative localization of sparsely activated molecules, which generally leads to a long acquisition time. By implementing advanced algorithms to treat overlapping point spread functions (PSFs), imaging of densely activated molecules can improve the limited temporal resolution, as has been well demonstrated in two-dimensional imaging. However, three-dimensional (3D) localization of high-density data remains challenging since PSFs are far more similar along the axial dimension than the lateral dimensions. Here, we present a new, high-density 3D imaging system and algorithm. The hybrid system is implemented by combining astigmatic and biplane imaging. The proposed 3D reconstruction algorithm is extended from our state-of-the art 2D high-density localization algorithm. Using mutual coherence analysis of model PSFs, we validated that the hybrid system is more suitable than astigmatic or biplane imaging alone for 3D localization of high-density data. The efficacy of the proposed method was confirmed via simulation and real data of microtubules. Furthermore, we also successfully demonstrated fluorescent-protein-based live cell 3D localization microscopy with a temporal resolution of just 3 seconds, capturing fast dynamics of the endoplasmic recticulum. (C) 2014 Optical Society of America

Optical Soc Amer2014

Chargement

Afficher plus