scholarly journals Global fitting for high-accuracy multi-channel single-molecule localization

2021 ◽  
Author(s):  
Yiming Li ◽  
Wei Shi ◽  
Sheng Liu ◽  
Ulf Matti ◽  
Decheng Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Maximum Information ◽  
Channel Detection ◽  
Fitting Algorithm ◽  
Localization Precision ◽  
Color Assignment ◽  
Graphics Processing ◽  
Global Fitting

Multi-channel detection in single-molecule localization microscopy (SMLM) greatly increases information content for various biological applications. Here, we present globLoc, a graphics processing unit (GPU) based global fitting algorithm with flexible PSF modeling and parameter sharing, to extract maximum information from multi-channel single molecule data. We show, both in simulations and experiments, that global fitting can substantially improve the 3D localization precision for biplane and 4Pi SMLM and color assignment for ratiometric multicolor imaging.

scholarly journals Ratiometric 4Pi single molecule localization with optimal resolution and color assignment

2021 ◽  
Author(s):  
Yiming Li ◽  
Jianwei Chen ◽  
Benxi Yao ◽  
Zhichao Yang ◽  
Wei Shi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Simulated Data ◽  
Color Separation ◽  
Optimal Resolution ◽  
Phase Interference ◽  
Localization Precision ◽  
Imaging Strategy ◽  
Color Assignment ◽  
Multi Phase ◽  
Global Fitting

4Pi single molecule localization microscopy (4Pi-SMLM) with two opposing objectives achieves sub-10 nm isotropic 3D resolution with as few as 250 photons collected by each objective. Here, we developed a new ratiometric multi-color imaging strategy for 4Pi-SMLM which employed the intrinsic multi-phase interference intensity without increasing the complexity of the system and achieved both optimal 3D resolution and color separation. By partially linking the photon parameters between channels with interference difference of π during global fitting of the multi-channel 4Pi single molecule data, we showed on simulated data that the loss of the localization precision is minimal compared with the theoretical minimum uncertainty, the Cramer-Rao lower bound (CRLB).

Implementing wide baseline matching algorithms on a graphics processing unit.

2007 ◽  
Author(s):  
Fredrick H. Rothganger ◽  
Kurt W. Larson ◽  
Antonio Ignacio Gonzales ◽  
Daniel S. Myers
Keyword(s):  
Graphics Processing Unit ◽  
Processing Unit ◽  
Wide Baseline Matching ◽  
Graphics Processing

scholarly journals Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

2021 ◽  
Vol 22 (10) ◽  
pp. 5212
Author(s):  
Andrzej Bak
Keyword(s):  
Molecular Conformation ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Diverse Range ◽  
Current State ◽  
Gpu Clusters ◽  
Pharmacophore Hypothesis ◽  
Rising Power ◽  
Graphics Processing ◽  
Ligand Conformation

A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.

Real-time, High-resolution Depth Upsampling on Embedded Accelerators

2021 ◽  
Vol 20 (3) ◽  
pp. 1-22
Author(s):  
David Langerman ◽  
Alan George
Keyword(s):  
High Resolution ◽  
Low Power ◽  
Real Time ◽  
Mixed Reality ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Reconfigurable Logic ◽  
Depth Sensors ◽  
Time Requirements ◽  
Graphics Processing

High-resolution, low-latency apps in computer vision are ubiquitous in today’s world of mixed-reality devices. These innovations provide a platform that can leverage the improving technology of depth sensors and embedded accelerators to enable higher-resolution, lower-latency processing for 3D scenes using depth-upsampling algorithms. This research demonstrates that filter-based upsampling algorithms are feasible for mixed-reality apps using low-power hardware accelerators. The authors parallelized and evaluated a depth-upsampling algorithm on two different devices: a reconfigurable-logic FPGA embedded within a low-power SoC; and a fixed-logic embedded graphics processing unit. We demonstrate that both accelerators can meet the real-time requirements of 11 ms latency for mixed-reality apps. 1

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