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MRI analysis for hippocampus segmentation on a distributed infrastructure

S. Tangaro, N. Amoroso, M. Antonacci, M. Boccardi, M. Bocchetta, A. Chincarini, D. Diacono, G. Donvito, R. Errico, G. B. Frisoni, T. Maggipinto, A. Monaco (+3 others)
2016 2016 IEEE International Symposium on Medical Measurements and Applications (MeMeA)  
However this technology requires a distributed computing infrastructure (such as Grid or Cloud) to be executed efficiently.  ...  In this paper we implemented a complete segmentation pipeline in brain magnetic resonance imaging (MRI).  ...  The manual segmentation on MRI is widely considered the gold signature for the hippocampal volume, however automated segmentation tools are mandatory because manual segmentation is a time-consuming task  ... 
doi:10.1109/memea.2016.7533716 dblp:conf/memea/TangaroAABBCDDE16 fatcat:yvd6ddajyfawdej6nzmwjthepe

A game for crowdsourcing the segmentation of BigBrain data

Arno Klein
2016 Research Ideas and Outcomes  
Both these systems opperate on cloud-based infrastructure.  ...  The principal aim of this proposal is to crowdsource the segmentation of cytoarchitectonic regions by means of a computer game, to transform an arduous, isolated task performed by experts into an engaging  ...  PICSL leads the development of other significant open-source tools, including interactive image segmentation tool ITK-SNAP, deformable image registration package ANTS/SyN, and diffusion MRI analysis package  ... 
doi:10.3897/rio.2.e8816 fatcat:jmilpqohufdtndugsmdqyp65py

Qualitative and Quantitative Comparison of Hippocampal Volumetric Software Applications: Do All Roads Lead to Rome?

Stephanie Mangesius, Lukas Haider, Lukas Lenhart, Ruth Steiger, Ferran Prados Carrasco, Christoph Scherfler, Elke R. Gizewski
2022 Biomedicines  
), Similarity-and-Truth-Estimation-for-Propagated-Segmentations (STEPS), and Quantib™.  ...  Comparing against the mean of all methods, moderate to low agreement was present considering categorization of hippocampal volumes into quartiles.  ...  GIF [27, 28] and STEPS [29] use a template library with associated manual segmentations including 682 brain and 110 hippocampal manual segmentations, which makes it reliable for hippocampal segmentations  ... 
doi:10.3390/biomedicines10020432 pmid:35203641 pmcid:PMC8962257 fatcat:lclr2yhctfdjlhfbly4cjdrsje

Management and Quality Control of Large Neuroimaging Datasets: Developments From the Barcelonaβeta Brain Research Center

Jordi Huguet, Carles Falcon, David Fusté, Sergi Girona, David Vicente, José Luis Molinuevo, Juan Domingo Gispert, Grégory Operto, for the ALFA Study
2021 Frontiers in Neuroscience  
Such a model gave rise to an ecosystem of tools aiming at improved quality control through seamless automatic processes combined with a variety of code libraries, command line tools, graphical user interfaces  ...  Collecting, hosting, managing, processing, or reviewing those datasets is typically achieved through a local neuroinformatics infrastructure.  ...  The upper part displays a zoomable snapshot (here a segmentation of hippocampal subfields).  ... 
doi:10.3389/fnins.2021.633438 pmid:33935631 pmcid:PMC8081968 fatcat:pg4eebsowzfybf2rjbcx7x5zae

Radiogenomics for Precision Medicine With A Big Data Analytics Perspective

Andreas S. Panayides, Marios Pattichis, Stephanos Leandrou, Costas Pitris, Anastasia Constantinidou, Constantinos S. Pattichis
2019 IEEE journal of biomedical and health informatics  
radiomics and radiogenomics by reviewing the case studies of Cancer and Alzheimer's disease, describe the computational challenges from a big data analytics perspective, and discuss standardization and open  ...  Hippocampal subfield analysis was also performed and it was shown that a locus within the MSRB3 gene could affect the dentate gyrus, subiculum, CA1 and fissure.  ...  Nvidia DIGITS [68] , Amazon Elastic Compute Cloud (EC2), Google Cloud, Microsoft Azure) that also facilitate an off the shelf solution to the computationally intensive processes that are often involved  ... 
doi:10.1109/jbhi.2018.2879381 pmid:30596591 fatcat:rqmjhmdmr5h3rdaody264ogs24

A Process for Digitizing and Simulating Biologically Realistic Oligocellular Networks Demonstrated for the Neuro-Glio-Vascular Ensemble

Jay S Coggan, Corrado Calì, Daniel Keller, Marco Agus, Daniya Boges, Marwan Abdellah, Kalpana Kare, Heikki Lehväslaiho, Stefan Eilemann, Renaud Blaise Jolivet, Markus Hadwiger, Henry Markram (+2 others)
2018 Frontiers in Neuroscience  
of electron micrographs, advanced data analysis tools, computational simulations and in silico visualization software.  ...  One will not understand the brain without an integrated exploration of structure and function, these attributes being two sides of the same coin: together they form the currency of biological computation  ...  The size and complexity of image data prevent an easy, on-line use of automated or semi-automated segmentation tools, proving an immediate feedback (within seconds) of the segmented structures; at the  ... 
doi:10.3389/fnins.2018.00664 pmid:30319342 pmcid:PMC6171468 fatcat:jnoqbjo6urecbopv2n35xbyel4

Evolving Applications, Technological Challenges and Future Opportunities in Neuromodulation: Proceedings of the Fifth Annual Deep Brain Stimulation Think Tank

Adolfo Ramirez-Zamora, James J. Giordano, Aysegul Gunduz, Peter Brown, Justin C. Sanchez, Kelly D. Foote, Leonardo Almeida, Philip A. Starr, Helen M. Bronte-Stewart, Wei Hu, Cameron McIntyre, Wayne Goodman (+25 others)
2018 Frontiers in Neuroscience  
According to the segmentation, a mean of 63.9% of modeled lesion volume within the ALIC intersected with the BA11 region.  ...  A literature review revealed five stereotactic targets within the ALIC. Targets were modeled as 5 mm spheres and were evaluated for overlap with various DTI-defined ALIC segments.  ... 
doi:10.3389/fnins.2017.00734 pmid:29416498 pmcid:PMC5787550 fatcat:24zvpf5ndbcrhhcy7xdrcinaby

Semi-automated registration-based anatomical labelling, voxel based morphometry and cortical thickness mapping of the mouse brain

Marco Pagani, Mario Damiano, Alberto Galbusera, Sotirios A. Tsaftaris, Alessandro Gozzi
2016 Journal of Neuroscience Methods  
All the computational steps have been carried out using tools and algorithms implemented within the ANTs toolkit (version 1.9 and employed to process 3D RARE morphoanatomical  ...  streamline and accelerate image processing time by exploiting large high-performancecomputing infrastructures.  ... 
doi:10.1016/j.jneumeth.2016.04.007 pmid:27079699 fatcat:wofk7oadk5acdi3eeb5lkbhmou

Integrating Brain Implants With Local and Distributed Computing Devices: A Next Generation Epilepsy Management System

Vaclav Kremen, Benjamin H. Brinkmann, Inyong Kim, Hari Guragain, Mona Nasseri, Abigail L. Magee, Tal Pal Attia, Petr Nejedly, Vladimir Sladky, Nathanial Nelson, Su-Youne Chang, Jeffrey A. Herron (+15 others)
2018 IEEE Journal of Translational Engineering in Health and Medicine  
In this paper, we describe a next-generation epilepsy management system that integrates local handheld and cloud-computing resources wirelessly coupled to an implanted device with embedded payloads (sensors  ...  Brain stimulation has emerged as an effective treatment for a wide range of neurological and psychiatric diseases.  ...  The authors also want to acknowledge Joost Wagenaar from Blackfynn Inc. for project related data management on Blackfynn cloud system. Greg Worrell and Mayo Clinic have equity in Blackfynn Inc.  ... 
doi:10.1109/jtehm.2018.2869398 pmid:30310759 pmcid:PMC6170139 fatcat:ohhfefkyujau5jmn2wdxf44bdi

CUBIC-Cloud: An Integrative Computational Framework Towards Community-Driven Whole-Mouse-Brain Mapping [article]

Tomoyuki Mano, Ken Murata, Kazuhiro Kon, Chika Shimizu, Hiroaki Ono, Shoi Shi, Rikuhiro G. Yamada, Kazunari Miyamichi, Etsuo A. Susaki, Kazushige Touhara, Hiroki R. Ueda
2020 bioRxiv   pre-print
Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.  ...  With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets.  ...  The core of the point cloud rendering engine was adopted from the open-source37 project, Potree [69].  ... 
doi:10.1101/2020.08.28.271031 fatcat:loqx2orlqbhpnkmet7kpmflcmy

Program Book

2020 2020 5th International Conference on Universal Village (UV)  
In this paper, we classified the patterns of clouds into four types (sugar, flower, fish, and gravel) proposed by Rasp et al. and performed image segmentation.  ...  However, in an intranet environment where Internet access is not possible, online map tools will not be available.  ... 
doi:10.1109/uv50937.2020.9426196 fatcat:bikzcbilgbfp5jzssihjmswpua

Predicting synaptic connectivity for large-scale microcircuit simulations using Snudda [article]

Johannes Hjorth, Jeanette Hellgren, Alexander Kozlov
2021 bioRxiv   pre-print
Here we describe an open source pipeline, using the software Snudda, for predicting microcircuit connectivity and for setting up simulations using the NEURON simulation environment in a reproducible way  ...  Simulation of large-scale networks of neurons is an important approach to understanding and interpreting experimental data from healthy and diseased brains.  ...  Acknowledgements: The simulations were performed on resources provided by the Swedish National Infrastructure for Computing at PDC (Center for Parallel Computing). We  ... 
doi:10.1101/2021.04.15.439985 fatcat:sfnevxpucnccpeimt2vo4v2kh4

Defense Advanced Research Projects Agency (Darpa) Fiscal Year 2015 Budget Estimates

Department Of Defense Comptroller's Office
2014 Zenodo  
An emphasis in the FY 2015 budget request focuses on research to tailor treatments to patients' unique characteristics, known as "precision medicine."  ...  The budget request details the proposed investments $80 million to develop new sets of tools for imaging and analytics of neural and synaptic brain activities that will improve diagnosis and care of wounded  ...  The program seeks to create an open-source development infrastructure for the aggregation of designer inputs applicable to complex electromechanical systems as well as software, and to exercise this infrastructure  ... 
doi:10.5281/zenodo.1215345 fatcat:fjzhmynqjbaafk67q2ckcblj2m

NetPyNE: a tool for data-driven multiscale modeling of brain circuits [article]

Salvador Dura-Bernal, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, George L Chadderdon, Cliff C Kerr, Samuel A Neymotin, Robert McDougal, Michael Hines (+2 others)
2018 bioRxiv   pre-print
The NetPyNE tool ( provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON.  ...  GUI is implemented on top of Geppetto, 95 an open-source platform that provides the 563 infrastructure for building tools for visualizing neuroscience models and data and managing simulations in 564 a  ...  including Brian, 55 MOOSE, 56, 57 PyNN, 17 Bionet 20 or Open Source 291 Brain. 29 Similarly simulations from these other tools can be imported into NetPyNE .  ... 
doi:10.1101/461137 fatcat:ar44ueohjvcubdnjgt54ilev3m

On the objectivity, reliability, and validity of deep learning enabled bioimage analyses

Dennis Segebarth, Matthias Griebel, Nikolai Stein, Cora R von Collenberg, Corinna Martin, Dominik Fiedler, Lucas B Comeras, Anupam Sah, Victoria Schoeffler, Teresa Lüffe, Alexander Dürr, Rohini Gupta (+8 others)
2020 eLife  
An analysis pipeline integrating data annotation, ground truth estimation, and model training can mitigate this risk.  ...  open-source Python library that is easily accessible for 521 both local installation or cloud-based deployment.  ...  experience across labs in an open science community.  ... 
doi:10.7554/elife.59780 pmid:33074102 pmcid:PMC7710359 fatcat:lyys35itobg3neink4tk7oiyue
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