MCX Cloud—a modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing

Fang, Qianqian; Yan, Song Y.

doi:10.1117/1.jbo.27.8.083008

Cited by 31 publications

(18 citation statements)

References 24 publications

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“… 225 Monte Carlo methods have traditionally also been computationally expensive, but they are now reaching higher speeds with deployment on GPU and cloud-based servers. 241 …”

Section: Discussionmentioning

confidence: 99%

Noninvasive hemoglobin sensing and imaging: optical tools for disease diagnosis

et al. 2022

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. Significance: Measurement and imaging of hemoglobin oxygenation are used extensively in the detection and diagnosis of disease; however, the applied instruments vary widely in their depth of imaging, spatiotemporal resolution, sensitivity, accuracy, complexity, physical size, and cost. The wide variation in available instrumentation can make it challenging for end users to select the appropriate tools for their application and to understand the relative limitations of different methods. Aim: We aim to provide a systematic overview of the field of hemoglobin imaging and sensing. Approach: We reviewed the sensing and imaging methods used to analyze hemoglobin oxygenation, including pulse oximetry, spectral reflectance imaging, diffuse optical imaging, spectroscopic optical coherence tomography, photoacoustic imaging, and diffuse correlation spectroscopy. Results: We compared and contrasted the ability of different methods to determine hemoglobin biomarkers such as oxygenation while considering factors that influence their practical application. Conclusions: We highlight key limitations in the current state-of-the-art and make suggestions for routes to advance the clinical use and interpretation of hemoglobin oxygenation information.

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“… 225 Monte Carlo methods have traditionally also been computationally expensive, but they are now reaching higher speeds with deployment on GPU and cloud-based servers. 241 …”

Section: Discussionmentioning

confidence: 99%

Noninvasive hemoglobin sensing and imaging: optical tools for disease diagnosis

et al. 2022

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“…4(a) , as an example to illustrate the simplicity of using JSON/JMesh data annotations to store mesh data. Because the JMesh format is built upon the JData specification 37 , 43 —a lightweight standard using JSON to annotate scientific data, JMesh mesh data constructs also support strongly-typed array [see Fig. 4(c) ] and record-level binary data compression 43 [see Fig.…”

Section: Blenderphotonics Interface Design and Key Featuresmentioning

confidence: 99%

“…This module calls Iso2Mesh to automatically tessellate a 3D volume stored in the NIfTI, 39 JNIfTI, 40 or MATLAB.mat formats, and output a surface mesh model for subsequent processing. NIfTI is an open standard to store MRI/fMRI scans and is widely supported in the field of neuroimaging; JNIfTI is a standardized 40 JSON wrapper 43 to the NIfTI format to enable human-readability, easy extension, and data exchange between neuroimaging tools. By calling the streamlined mesh generation function in Iso2Mesh, the 3D volume data from a JNIfTI/NIfTI file can be preprocessed to create both tetrahedral volume mesh as well as surface mesh that is at the outer surface of the volume mesh.…”

Section: Blenderphotonics Interface Design and Key Featuresmentioning

confidence: 99%

BlenderPhotonics: an integrated open-source software environment for three-dimensional meshing and photon simulations in complex tissues

Zhang

Fang

2022

J. Biomed. Opt.

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. Significance : Rapid advances in biophotonics techniques require quantitative, model-based computational approaches to obtain functional and structural information from increasingly complex and multiscaled anatomies. The lack of efficient tools to accurately model tissue structures and subsequently perform quantitative multiphysics modeling greatly impedes the clinical translation of these modalities. Aim : Although the mesh-based Monte Carlo (MMC) method expands our capabilities in simulating complex tissues using tetrahedral meshes, the generation of such domains often requires specialized meshing tools, such as Iso2Mesh. Creating a simplified and intuitive interface for tissue anatomical modeling and optical simulations is essential toward making these advanced modeling techniques broadly accessible to the user community. Approach : We responded to the above challenge by combining the powerful, open-source three-dimensional (3D) modeling software, Blender, with state-of-the-art 3D mesh generation and MC simulation tools, utilizing the interactive graphical user interface in Blender as the front-end to allow users to create complex tissue mesh models and subsequently launch MMC light simulations. Results : Here, we present a tutorial to our Python-based Blender add-on—BlenderPhotonics—to interface with Iso2Mesh and MMC, which allows users to create, configure and refine complex simulation domains and run hardware-accelerated 3D light simulations with only a few clicks. We provide a comprehensive introduction to this tool and walk readers through five examples, ranging from simple shapes to sophisticated realistic tissue models. Conclusions : BlenderPhotonics is user friendly and open source, and it leverages the vastly rich ecosystem of Blender. It wraps advanced modeling capabilities within an easy-to-use and interactive interface. The latest software can be downloaded at http://mcx.space/bp .

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“… 7 modify the ESG5 high energy electron and photon MC simulator to run a subset of the photons on each node in an AWS cluster; the lower-energy photons in PDT cannot be accurately simulated in this system. The most comparable work to ours is the MCX Cloud tool suite 24 which (such as our tools) simulates photon transport in biological tissues. Unlike MCX cloud, we use a public (AWS) cloud instead of a private cluster, and our tool suite includes not only Monte Carlo simulation of photon transport but also optimization of iPDT.…”

Section: Introductionmentioning

confidence: 99%

Scalable and accessible personalized photodynamic therapy optimization with FullMonte and PDT-SPACE

Wang

Dai

et al. 2022

J. Biomed. Opt.

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. Significance: Open-source software packages have been extensively used in the past three decades in medical imaging and diagnostics, aiming to study the feasibility of the application ex vivo . Unfortunately, most of the existing open-source tools require some software engineering background to install the prerequisite libraries, choose a suitable computational platform, and combine several software tools to address different applications. Aim: To facilitate the use of open-source software in medical applications, enabling computational studies of treatment outcomes prior to the complex in-vivo setting. Approach: FullMonteWeb, an open-source, user-friendly web-based software with a graphical user interface for interstitial photodynamic therapy (iPDT) modeling, visualization, and optimization, is introduced. The software can perform Monte Carlo simulations of light propagation in biological tissues, along with iPDT plan optimization. FullMonteWeb installs and runs the required software and libraries on Amazon Web Services (AWS), allowing scalable computing without complex set up. Results: FullMonteWeb allows simulation of large and small problems on the most appropriate compute hardware, enabling cost improvements of versus always running on a single platform. Case studies in optical property estimation and diffuser placement optimization highlight FullMonteWeb’s versatility. Conclusion: The FullMonte open source suite enables easier and more cost-effective in-silico studies for iPDT.

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MCX Cloud—a modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing

Cited by 31 publications

References 24 publications

Noninvasive hemoglobin sensing and imaging: optical tools for disease diagnosis

Noninvasive hemoglobin sensing and imaging: optical tools for disease diagnosis

BlenderPhotonics: an integrated open-source software environment for three-dimensional meshing and photon simulations in complex tissues

Scalable and accessible personalized photodynamic therapy optimization with FullMonte and PDT-SPACE

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