PMID- 35781968
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220716
IS  - 2156-7085 (Print)
IS  - 2156-7085 (Electronic)
IS  - 2156-7085 (Linking)
VI  - 13
IP  - 6
DP  - 2022 Jun 1
TI  - PCIe-based FPGA-GPU heterogeneous computation for real-time multi-emitter fitting 
      in super-resolution localization microscopy.
PG  - 3401-3415
LID - 10.1364/BOE.459198 [doi]
AB  - Real-time multi-emitter fitting is a key technology for advancing 
      super-resolution localization microscopy (SRLM), especially when it is necessary 
      to achieve dynamic imaging quality control and/or optimization of experimental 
      conditions. However, with the increase of activation densities, the requirements 
      in the computing resources would increase rapidly due to the complexity of the 
      fitting algorithms, making it difficult to realize real-time multi-emitter 
      fitting for emitter density more than 0.6 mol/microm(2) in large field of view (FOV), 
      even after acceleration with the popular Graphics Processing Unit (GPU) 
      computation. Here we adopt the task parallelism strategy in computer science to 
      construct a Peripheral Component Interconnect Express (PCIe) based all-in-one 
      heterogeneous computing platform (AIO-HCP), where the data between two major 
      parallel computing hardware, Field Programmable Gate Array (FPGA) and GPU, are 
      interacted directly and executed simultaneously. Using simulated and experimental 
      data, we verify that AIO-HCP could achieve a data throughput of up to  approximately  1.561 
      GB/s between FPGA and GPU. With this new platform, we develop a multi-emitter 
      fitting method, called AIO-STORM, under big data stream parallel scheduling. We 
      show that AIO-STORM is capable of providing real-time image processing on raw 
      images with 100 microm x 100 microm FOV, 10 ms exposure time and 5.5 mol/microm(2) structure 
      density, without scarifying image quality. This study overcomes the data 
      throughput limitation of heterogeneous devices, demonstrates the power of the 
      PCIe-based heterogeneous computation platform, and offers opportunities for 
      multi-scale stitching of super-resolution images.
CI  - (c) 2022 Optica Publishing Group under the terms of the Optica Open Access 
      Publishing Agreement.
FAU - Gui, Dan
AU  - Gui D
AUID- ORCID: 0000-0003-2935-6732
AD  - Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of 
      Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong 
      University of Science and Technology, Wuhan 430074, China.
AD  - School of Electronic Engineering, Wuhan Vocational College of Software and 
      Engineering, Wuhan 430205, China.
AD  - dgui@hust.edu.cn.
FAU - Chen, Yunjiu
AU  - Chen Y
AD  - Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of 
      Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong 
      University of Science and Technology, Wuhan 430074, China.
FAU - Kuang, Weibing
AU  - Kuang W
AD  - Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of 
      Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong 
      University of Science and Technology, Wuhan 430074, China.
FAU - Shang, Mingtao
AU  - Shang M
AD  - Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of 
      Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong 
      University of Science and Technology, Wuhan 430074, China.
FAU - Zhang, Yingjun
AU  - Zhang Y
AD  - Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical 
      Engineering, Hainan University, Haikou 570228, China.
FAU - Huang, Zhen-Li
AU  - Huang ZL
AUID- ORCID: 0000-0003-2400-966X
AD  - Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical 
      Engineering, Hainan University, Haikou 570228, China.
AD  - Huang2020@hainanu.edu.cn.
LA  - eng
PT  - Journal Article
DEP - 20220516
PL  - United States
TA  - Biomed Opt Express
JT  - Biomedical optics express
JID - 101540630
PMC - PMC9208611
COIS- Chinese patent (No. 201810410930.2).
EDAT- 2022/07/06 06:00
MHDA- 2022/07/06 06:01
PMCR- 2022/06/01
CRDT- 2022/07/05 09:43
PHST- 2022/04/11 00:00 [received]
PHST- 2022/05/07 00:00 [revised]
PHST- 2022/05/09 00:00 [accepted]
PHST- 2022/07/05 09:43 [entrez]
PHST- 2022/07/06 06:00 [pubmed]
PHST- 2022/07/06 06:01 [medline]
PHST- 2022/06/01 00:00 [pmc-release]
AID - 459198 [pii]
AID - 10.1364/BOE.459198 [doi]
PST - epublish
SO  - Biomed Opt Express. 2022 May 16;13(6):3401-3415. doi: 10.1364/BOE.459198. 
      eCollection 2022 Jun 1.