Evidence map›Paper›PMID 35614533›Full record

ArticleJournal of biomedical optics2022

Framework for denoising Monte Carlo photon transport simulations using deep learning.

Matin Raayai Ardakani, Leiming Yu, David Kaeli, Qianqian Fang

Abstract read
In one paragraph

Article in Journal of biomedical optics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Quantitative analysis of the optogenetic excitability of CA1 neurons.Frontiers in computational neuroscience · 2023
    Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Matin Raayai ArdakaniNortheastern Univ., United States.
Leiming YuAnalogic Corp., United States.
David KaeliNortheastern Univ., United States.
Qianqian FangNortheastern Univ., United States.

Funding

Next-generation Monte Carlo eXtreme Light Transport Simulation PlatformR01GM114365 · NIGMS · NORTHEASTERN UNIVERSITY · PI FANG, QIANQIAN · 2015 to 2023
$2.9M
Ultra-high-density, compressive and media- adaptive optical breast tomography platformR01CA204443 · NCI · NORTHEASTERN UNIVERSITY · PI FANG, QIANQIAN · 2016 to 2025
$2.5M
Next-generation optical brain functional imaging platformR01EB026998 · NIBIB · NORTHEASTERN UNIVERSITY · PI FANG, QIANQIAN · 2018 to 2019
$870k
NCI NIH HHS R01 CA204443NIBIB NIH HHS R01 EB026998NIGMS NIH HHS R01 GM114365
6 · The paper itself

Abstract

significanceThe Monte Carlo (MC) method is widely used as the gold-standard for modeling light propagation inside turbid media, such as human tissues, but combating its inherent stochastic noise requires one to simulate a large number photons, resulting in high computational burdens.

aimWe aim to develop an effective image denoising technique using deep learning (DL) to dramatically improve the low-photon MC simulation result quality, equivalently bringing further acceleration to the MC method. APPROACH: We developed a cascade-network combining DnCNN with UNet, while extending a range of established image denoising neural-network architectures, including DnCNN, UNet, DRUNet, and deep residual-learning for denoising MC renderings (ResMCNet), in handling three-dimensional MC data and compared their performances against model-based denoising algorithms. We also developed a simple yet effective approach to creating synthetic datasets that can be used to train DL-based MC denoisers.

resultsOverall, DL-based image denoising algorithms exhibit significantly higher image quality improvements over traditional model-based denoising algorithms. Among the tested DL denoisers, our cascade network yields a 14 to 19 dB improvement in signal-to-noise ratio, which is equivalent to simulating 25  ×   to 78  ×   more photons. Other DL-based methods yielded similar results, with our method performing noticeably better with low-photon inputs and ResMCNet along with DRUNet performing better with high-photon inputs. Our cascade network achieved the highest quality when denoising complex domains, including brain and mouse atlases.

conclusionsIncorporating state-of-the-art DL denoising techniques can equivalently reduce the computation time of MC simulations by one to two orders of magnitude. Our open-source MC denoising codes and data can be freely accessed at http://mcx.space/.

Indexed as

Deep LearningPhotonsAlgorithmsAnimalsImage Processing, Computer-AssistedMiceMonte Carlo MethodNeural Networks, ComputerSignal-To-Noise Ratioconvolutional neural networksdeep learningimage denoisingMonte Carlo methodphoton transport

Identifiers

PMID35614533
PMCPMC9130925

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.