Literature DB >> 27498015

Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.

Tina Kapur1, Steve Pieper2, Andriy Fedorov3, J-C Fillion-Robin4, Michael Halle3, Lauren O'Donnell3, Andras Lasso5, Tamas Ungi5, Csaba Pinter5, Julien Finet4, Sonia Pujol3, Jayender Jagadeesan3, Junichi Tokuda3, Isaiah Norton3, Raul San Jose Estepar3, David Gering6, Hugo J W L Aerts3, Marianna Jakab3, Nobuhiko Hata3, Luiz Ibanez7, Daniel Blezek8, Jim Miller9, Stephen Aylward4, W Eric L Grimson10, Gabor Fichtinger5, William M Wells3, William E Lorensen11, Will Schroeder4, Ron Kikinis3.   

Abstract

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.
Copyright © 2016 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  3D Slicer; Hackathon; Medical image computing; NA-MIC; Open access; Open science; Open source; Project week; Reproducible research

Mesh:

Year:  2016        PMID: 27498015      PMCID: PMC5003088          DOI: 10.1016/j.media.2016.06.035

Source DB:  PubMed          Journal:  Med Image Anal        ISSN: 1361-8415            Impact factor:   8.545


  1 in total

1.  Policy: NIH plans to enhance reproducibility.

Authors:  Francis S Collins; Lawrence A Tabak
Journal:  Nature       Date:  2014-01-30       Impact factor: 49.962

  1 in total
  13 in total

1.  SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality.

Authors:  Csaba Pinter; Andras Lasso; Saleh Choueib; Mark Asselin; Jean-Christophe Fillion-Robin; Jean-Baptiste Vimort; Ken Martin; Matthew A Jolley; Gabor Fichtinger
Journal:  IEEE Trans Med Robot Bionics       Date:  2020-03-26

2.  Retrospective evaluation and SEEG trajectory analysis for interactive multi-trajectory planner assistant.

Authors:  Davide Scorza; Elena De Momi; Lisa Plaino; Gaetano Amoroso; Gabriele Arnulfo; Massimo Narizzano; Luis Kabongo; Francesco Cardinale
Journal:  Int J Comput Assist Radiol Surg       Date:  2017-07-14       Impact factor: 2.924

3.  Anatomical Region Segmentation for Objective Surgical Skill Assessment with Operating Room Motion Data.

Authors:  Yangming Li; Randall A Bly; R Alex Harbison; Ian M Humphreys; Mark E Whipple; Blake Hannaford; Kris S Moe
Journal:  J Neurol Surg B Skull Base       Date:  2017-07-31

Review 4.  A community-based approach to image analysis of cells, tissues and tumors.

Authors:  Juan Carlos Vizcarra; Erik A Burlingame; Clemens B Hug; Yury Goltsev; Brian S White; Darren R Tyson; Artem Sokolov
Journal:  Comput Med Imaging Graph       Date:  2021-11-19       Impact factor: 4.790

5.  Practical methods for segmentation and calculation of brain volume and intracranial volume: a guide and comparison.

Authors:  Thomas Harkey; David Baker; John Hagen; Hayden Scott; Viktoras Palys
Journal:  Quant Imaging Med Surg       Date:  2022-07

6.  Machine learning based analysis of stroke lesions on mouse tissue sections.

Authors:  Gerasimos Damigos; Evangelia I Zacharaki; Nefeli Zerva; Angelos Pavlopoulos; Konstantina Chatzikyrkou; Argyro Koumenti; Konstantinos Moustakas; Constantinos Pantos; Iordanis Mourouzis; Athanasios Lourbopoulos
Journal:  J Cereb Blood Flow Metab       Date:  2022-02-25       Impact factor: 6.960

7.  The Effect of Registration on Voxel-Wise Tofts Model Parameters and Uncertainties from DCE-MRI of Early-Stage Breast Cancer Patients Using 3DSlicer.

Authors:  Matthew Mouawad; Heather Biernaski; Muriel Brackstone; Michael Lock; Anat Kornecki; Olga Shmuilovich; Ilanit Ben-Nachum; Frank S Prato; R Terry Thompson; Stewart Gaede; Neil Gelman
Journal:  J Digit Imaging       Date:  2020-08-03       Impact factor: 4.056

8.  Preliminary Results of High-Precision Computed Diffusion Weighted Imaging for the Diagnosis of Hepatocellular Carcinoma at 3 Tesla.

Authors:  Motonori Akagi; Yuko Nakamura; Toru Higaki; Yoshiko Matsubara; Hiroaki Terada; Yukiko Honda; Fuminari Tatsugami; Yasutaka Baba; Makoto Iida; Kazuo Awai
Journal:  J Comput Assist Tomogr       Date:  2018 May/Jun       Impact factor: 1.826

9.  SlicerArduino: A Bridge between Medical Imaging Platform and Microcontroller.

Authors:  Paolo Zaffino; Alessio Merola; Domenico Leuzzi; Virgilio Sabatino; Carlo Cosentino; Maria Francesca Spadea
Journal:  Bioengineering (Basel)       Date:  2020-09-11

10.  SciKit-Surgery: compact libraries for surgical navigation.

Authors:  Stephen Thompson; Thomas Dowrick; Mian Ahmad; Goufang Xiao; Bongjin Koo; Ester Bonmati; Kim Kahl; Matthew J Clarkson
Journal:  Int J Comput Assist Radiol Surg       Date:  2020-05-20       Impact factor: 2.924

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