MCmatlab: an open-source, user-friendly, MATLAB-integrated three-dimensional Monte Carlo light transport solver with heat diffusion and tissue damage

To investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further inside the specimen as photons in deeper focus must traverse a longer distance within the specimen. This type of blur is called depth-variance. Moreover, due to lens imperfection, the blur has asymmetric shape. Most deconvolution solutions for removing blur assume depth-invariant or x-y symmetric blur, and presently, there is no open-source for depth-variant asymmetric deconvolution. In addition, existing datasets for deconvolution microscopy also assume invariant or x-y symmetric blur, which are insufficient to reflect actual imaging conditions. DVDeconv, that is a set of MATLAB functions with a user-friendly graphical interface, has been developed to address depth-variant asymmetric blur. DVDeconv includes dataset, depth-variant asymmetric point spread function generator, and deconvolution algorithms. Experimental results using DVDeconv reveal that depth-variant asymmetric deconvolution using DVDeconv removes blurs accurately. Furthermore, the dataset in DVDeconv constructed can be used to evaluate the performance of microscopy deconvolution to be developed in the future.

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GIANI: open-source software for automated analysis of 3D microscopy images

10.1101/2020.10.15.340810 ◽

2020 ◽

Author(s):

David J. Barry ◽

Claudia Gerri ◽

Donald M. Bell ◽

Rocco D’Antuono ◽

Kathy K. Niakan

Keyword(s):

Protein Expression ◽

Open Source ◽

Cell Fate ◽

Open Source Software ◽

High Performance ◽

Three Dimensional ◽

Automated Analysis ◽

Large Numbers ◽

User Friendly ◽

High Performance Computing Cluster

AbstractThe study of cellular and developmental processes in physiologically relevant three-dimensional (3D) systems facilitates an understanding of mechanisms underlying cell fate, disease and injury. While cutting-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a lack of user-friendly, open-source software to analyse such images. Here we describe GIANI (djpbarry.github.io/Giani), new software for the analysis of 3D images, implemented as a plugin for the popular FIJI platform. The design primarily facilitates segmentation of nuclei and cells, followed by quantification of morphology and protein expression. GIANI enables routine and reproducible batch-processing of large numbers of images and also comes with scripting and command line tools, such that users can incorporate its functionality into their own scripts and easily run GIANI on a high-performance computing cluster. We demonstrate the utility of GIANI by quantifying cell morphology and protein expression in mouse early embryos. More generally, we anticipate that GIANI will be a useful tool for researchers in a variety of biomedical fields.

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BlenderPhotonics - a versatile environment for 3-D complex bio-tissue modeling and light transport simulations based on Blender

10.1101/2022.01.12.476124 ◽

2022 ◽

Author(s):

Yuxuang Zhang ◽

Qianqian Fang

Keyword(s):

Open Source ◽

Structural Information ◽

Quantitative Model ◽

Light Transport ◽

Simulation Tools ◽

Modeling Software ◽

Anatomical Modeling ◽

Physics Modeling ◽

User Friendly ◽

Intuitive Interface

Significance: Rapid advances in biophotonics techniques require quantitative, model-based computational approaches to obtain functional and structural information from increasingly complex and multi-scaled anatomies. The lack of efficient tools to accurately model tissue structures and subsequently perform quantitative multi-physics modeling greatly impedes the clinical translation of these modalities. Aim: While the mesh-based Monte Carlo (MMC) method expands our capabilities in simulating complex tissues by 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 towards making these advanced modeling techniques broadly accessible to the user community. Approach: We responded to the above challenge by combining the powerful, open-source 3-D modeling software, Blender, with state-of-the-art 3-D mesh generation and MC simulation tools, utilizing the interactive graphical user interface (GUI) in Blender as the front-end to allow users to create complex tissue mesh models, and subsequently launch MMC light simulations. Results: We have developed a Python-based Blender add-on -- BlenderPhotonics -- to interface with Iso2Mesh and MMC, allowing users to create, configure and refine complex simulation domains and run hardware-accelerated 3-D light simulations with only a few clicks. In this tutorial, we provide a comprehensive introduction to this new tool and walk readers through 5 examples, ranging from simple shapes to sophisticated realistic tissue models. Conclusion: BlenderPhotonics is user-friendly and open-source, leveraging 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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MackDroid - An Android based Application to monitor devices

Journal of Communications Technology Electronics and Computer Science ◽

10.22385/jctecs.v9i0.130 ◽

2016 ◽

Vol 9 ◽

pp. 1

Author(s):

Maaz Sirkhot ◽

Ekta Sirwani ◽

Aishwarya Kourani ◽

Akshit Batheja ◽

Kajal Jethanand Jewani

Keyword(s):

Operating System ◽

Open Source ◽

Vital Role ◽

Mobile Users ◽

Android Application ◽

Web Page ◽

Technological World ◽

Monitoring Service ◽

User Friendly

In this technological world, smartphones can be considered as one of the most far-reaching inventions. It plays a vital role in connecting people socially. The number of mobile users using an Android based smartphone has increased rapidly since last few years resulting in organizations, cyber cell departments, government authorities feeling the need to monitor the activities on certain targeted devices in order to maintain proper functionality of their respective jobs. Also with the advent of smartphones, Android became one of the most popular and widely used Operating System. Its highlighting features are that it is user friendly, smartly designed, flexible, highly customizable and supports latest technologies like IoT. One of the features that makes it exclusive is that it is based on Linux and is Open Source for all the developers. This is the reason why our project Mackdroid is an Android based application that collects data from the remote device, stores it and displays on a PHP based web page. It is primarily a monitoring service that analyzes the contents and distributes it in various categories like Call Logs, Chats, Key logs, etc. Our project aims at developing an Android application that can be used to track, monitor, store and grab data from the device and store it on a server which can be accessed by the handler of the application.

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Fast Overlap Detection between Hard-Core Colloidal Cuboids and Spheres. The OCSI Algorithm

Algorithms ◽

10.3390/a14030072 ◽

2021 ◽

Vol 14 (3) ◽

pp. 72

Author(s):

Luca Tonti ◽

Alessandro Patti

Keyword(s):

Colloidal Particles ◽

Dynamic Properties ◽

Wide Spectrum ◽

Three Dimensional ◽

Hard Core ◽

Detection Algorithm ◽

Three Dimensional Objects ◽

Aggregation Behaviour ◽

Sphere Radius ◽

User Friendly

Collision between rigid three-dimensional objects is a very common modelling problem in a wide spectrum of scientific disciplines, including Computer Science and Physics. It spans from realistic animation of polyhedral shapes for computer vision to the description of thermodynamic and dynamic properties in simple and complex fluids. For instance, colloidal particles of especially exotic shapes are commonly modelled as hard-core objects, whose collision test is key to correctly determine their phase and aggregation behaviour. In this work, we propose the Oriented Cuboid Sphere Intersection (OCSI) algorithm to detect collisions between prolate or oblate cuboids and spheres. We investigate OCSI’s performance by bench-marking it against a number of algorithms commonly employed in computer graphics and colloidal science: Quick Rejection First (QRI), Quick Rejection Intertwined (QRF) and a vectorized version of the OBB-sphere collision detection algorithm that explicitly uses SIMD Streaming Extension (SSE) intrinsics, here referred to as SSE-intr. We observed that QRI and QRF significantly depend on the specific cuboid anisotropy and sphere radius, while SSE-intr and OCSI maintain their speed independently of the objects’ geometry. While OCSI and SSE-intr, both based on SIMD parallelization, show excellent and very similar performance, the former provides a more accessible coding and user-friendly implementation as it exploits OpenMP directives for automatic vectorization.

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Evaluating variability in coseismic slips of paleoearthquakes from an incomplete slip history: an example from displaced terrace flights across the Kamishiro fault, central Japan

Progress in Earth and Planetary Science ◽

10.1186/s40645-021-00407-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Naoya Takahashi ◽

Shinji Toda

Keyword(s):

Monte Carlo ◽

Three Dimensional ◽

Seismic Hazard Assessment ◽

Probabilistic Seismic Hazard Assessment ◽

Reverse Fault ◽

Central Japan ◽

Systematic Analysis ◽

Fluvial Terraces ◽

Rupture Length ◽

Slip History

AbstractExamining the regularity in slip over seismic cycles leads to an understanding of earthquake recurrence and provides the basis for probabilistic seismic hazard assessment. Systematic analysis of three-dimensional paleoseismic trenches and analysis of offset markers along faults reveal slip history. Flights of displaced terraces have also been used to study slips of paleoearthquakes when the number of earthquakes contributing to the observed displacement of a terrace is known. This study presents a Monte Carlo-based approach to estimating slip variability using displaced terraces when a detailed paleoseismic record is not available. First, we mapped fluvial terraces across the Kamishiro fault, which is an intra-plate reverse fault in central Japan, and systematically measured the cumulative dip slip of the mapped terraces. By combining these measurements with the age of the paleoearthquakes, we estimated the amount of dip slip for the penultimate event (PE) and antepenultimate event (APE) to be 1.6 and 3.4 m, respectively. The APE slip was nearly three times larger than the most recent event of 2014 (Mw 6.2): 1.2 m. This suggests that the rupture length of the APE was much longer than that of the 2014 event and the entire Kamishiro fault ruptured with adjacent faults during the APE. Thereafter, we performed the Monte Carlo simulations to explore the possible range of the coefficient of variation for slip per event (COVs). The simulation considered all the possible rupture histories in terms of the number of events and their slip amounts. The resulting COVs typically ranged between 0.3 and 0.54, indicating a large variation in the slip per event of the Kamishiro fault during the last few thousand years. To test the accuracy of our approach, we performed the same simulation to a fault whose slip per event was well constrained. The result showed that the error in the COVs estimate was less than 0.15 in 86% of realizations, which was comparable to the uncertainty in COVs derived from a paleoseismic trenching. Based on the accuracy test, we conclude that the Monte Carlo-based approach should help assess the regularity of earthquakes using an incomplete paleoseismic record.

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