Reconstruction From Multiple Poses in Fluorescence Imaging: Proof of Concept

Fortun, Denis; Guichard, Paul; Chu, Ning; Unser, Michaël

doi:10.1109/jstsp.2015.2493884

Cited by 4 publications

(6 citation statements)

References 40 publications

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“…Other studies that have made use of the same principles 4 6 8 have used custom software specialized for each particular study. General-purpose algorithms for the reconstruction of 3D data have been published 5 18 , although no software was provided.…”

Section: Discussionmentioning

confidence: 99%

Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper

Gray

Mercer

Henriques

2017

JoVE

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Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm allows for the routine imaging of nanoscale biological complexes and processes. This increase in resolution also means that methods popular in electron microscopy, such as single-particle analysis, can readily be applied to super-resolution fluorescence microscopy. By combining this analytical approach with super-resolution optical imaging, it becomes possible to take advantage of the molecule-specific labeling capacity of fluorescence microscopy to generate structural maps of molecular elements within a metastable structure. To this end, we have developed a novel algorithm — VirusMapper — packaged as an easy-to-use, high-performance, and high-throughput ImageJ plugin. This article presents an in-depth guide to this software, showcasing its ability to uncover novel structural features in biological molecular complexes. Here, we present how to assemble compatible data and provide a step-by-step protocol on how to use this algorithm to apply single-particle analysis to super-resolution images.

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Section: Discussionmentioning

confidence: 99%

Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper

Gray

Mercer

Henriques

2017

JoVE

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“…Secondly, they perform an average of particles that produces blurring artefacts. We highlighted this effect and how to reduce it with sparsity-based reconstruction [19].…”

Section: A Related Workmentioning

confidence: 99%

“…, H Nc ϑi ), where H c ϑi ∈ R N ×N is the PSF matrix of the channel indexed by c on which the inverse rotation of angle θ i has been applied. Then, the acquisition model for each aligned particle can be written (see [19] for a continuous derivation)…”

Section: Joint Single Volume Reconstruction and Pose Estimationmentioning

confidence: 99%

“…Three main tasks have to be realized: 1) Detection of the particles in the input volumes; 2) Estimation of the orientation of each particle; 3) Reconstruction of a common multichannel model. In previous work [19], we developed a method to address the third task and have already demonstrated the feasibility of the reconstruction for a large number of input particles. This proof of concept was realized merely on simulated data for a single channel, without particle detection and assuming known orientations.…”

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confidence: 99%

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Reconstruction From Multiple Particles for 3D Isotropic Resolution in Fluorescence Microscopy

Fortun

Guichard

Hamel

et al. 2018

IEEE Trans. Med. Imaging

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The imaging of proteins within macromolecular complexes has been limited by the low axial resolution of optical microscopes. To overcome this problem, we propose a novel computational reconstruction method that yields isotropic resolution in fluorescence imaging. The guiding principle is to reconstruct a single volume from the observations of multiple rotated particles. Our new operational framework detects particles, estimates their orientation, and reconstructs the final volume. The main challenge comes from the absence of initial template and a priori knowledge about the orientations. We formulate the estimation as a blind inverse problem, and propose a block-coordinate stochastic approach to solve the associated non-convex optimization problem. The reconstruction is performed jointly in multiple channels. We demonstrate that our method is able to reconstruct volumes with 3D isotropic resolution on simulated data. We also perform isotropic reconstructions from real experimental data of doubly labeled purified human centrioles. Our approach revealed the precise localization of the centriolar protein Cep63 around the centriole microtubule barrel. Overall, our method offers new perspectives for applications in biology that require the isotropic mapping of proteins within macromolecular assemblies.

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“…Our work is a proof of concept and a first step toward the realization of a complete and practical framework that would include Steps 1) and 2). More details about our method can be found in a longer version of this paper [8].…”

Section: Introductionmentioning

confidence: 99%

Isotropic resolution in fluorescence imaging by single particle reconstruction

Fortun

Guichard

Chu

et al. 2016

2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)

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Low axial resolution is a major limitation of fluorescence imaging modalities. We propose a methodology to achieve high isotropic resolution by reconstructing fluorescence volumes from observations of multiple particle replicates with different orientations. The challenge is to conciliate high reconstruction accuracy, requiring a large amount of input 3D data, with computational tractability. We achieve this goal by designing an iterative joint deconvolution and multiview reconstruction algorithm with an efficient augmentedLagrangian based optimization. The computational cost is limited to only two FFTs per iterations, regardless of the number of input particles. We also adopt the nuclear norm of the Hessian as regularizer to avoid the usual staircase artifacts of the more standard total-variation. Experimental validation on realistic simulated data demonstrate the efficiency and accuracy of our method.

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Reconstruction From Multiple Poses in Fluorescence Imaging: Proof of Concept

Cited by 4 publications

References 40 publications

Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper

Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper

Reconstruction From Multiple Particles for 3D Isotropic Resolution in Fluorescence Microscopy

Isotropic resolution in fluorescence imaging by single particle reconstruction

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