Open science – combining open data and open source software: Medical image analysis with the Insight Toolkit

2005 ◽  
Vol 9 (6) ◽  
pp. 503-506 ◽  
Author(s):  
Terry S. Yoo ◽  
Dimitris N. Metaxas
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Open Data ◽  
Open Science

scholarly journals Data, data everywhere, nor an image to read - Finding open image databases.

2007 ◽  
Author(s):  
David Holmes ◽  
Richard A Robb
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Medical Image ◽  
Open Data ◽  
Image Database ◽  
Open Science ◽  
Research Community ◽  
Image Databases ◽  
Software Methodologies

Open Science includes access to both open source software/methodologies and open data. While there has been progress in open image databases, the results of these efforts are under-reported. As such, imaging scientists are unaware of the available data. In addition, many researchers are interested in providing their data to the greater research community, but may be unaware of the process to release the data. The purpose of this paper is to describe our efforts in developing an open website which includes information on accessible medical image databases as well as some of the logistics for providing an open image database. Most importantly, the authors are requesting participation from the community to contribute to the Medical Image Database Repository (http://midr.org) in order to consolidate the collect knowledge of the community.

scholarly journals MIA - A free and open source software for gray scale medical image analysis

2013 ◽  
Vol 8 (1) ◽  
Author(s):  
Gert Wollny ◽  
Peter Kellman ◽  
María-Jesus Ledesma-Carbayo ◽  
Matthew M Skinner ◽  
Jean-Jaques Hublin ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Gray Scale

scholarly journals A brief introduction to Open Data, Open Source Software and Collective Intelligence for environmental data creators and users

2018 ◽  
Author(s):  
Tomislav Hengl ◽  
Ichsani Wheeler ◽  
Robert A MacMillan
Keyword(s):  
Open Access ◽  
Open Source ◽  
Open Source Software ◽  
Collective Intelligence ◽  
Open Data ◽  
Open Science ◽  
Environmental Data ◽  
Key Aspects

Using the term "Open data" has become a bit of a fashion, but using it without clear specifications is misleading i.e. it can be considered just an empty phrase. Probably even worse is the term "Open Science" — can science be NOT open at all? Are we reinventing something that should be obvious from start? This guide tries to clarify some key aspects of Open Data, Open Source Software and Crowdsourcing using examples of projects and business. It aims at helping you understand and appreciate complexity of Open Data, Open Source software and Open Access publications. It was specifically written for producers and users of environmental data, however, the guide will likely be useful to any data producers and user.

scholarly journals A brief introduction to Open Data, Open Source Software and Collective Intelligence for environmental data creators and users

2018 ◽  
Author(s):  
Tomislav Hengl ◽  
Ichsani Wheeler ◽  
Robert A MacMillan
Keyword(s):  
Open Access ◽  
Open Source ◽  
Open Source Software ◽  
Collective Intelligence ◽  
Open Data ◽  
Open Science ◽  
Environmental Data ◽  
Key Aspects

Using the term "Open data" has become a bit of a fashion, but using it without clear specifications is misleading i.e. it can be considered just an empty phrase. Probably even worse is the term "Open Science" — can science be NOT open at all? Are we reinventing something that should be obvious from start? This guide tries to clarify some key aspects of Open Data, Open Source Software and Crowdsourcing using examples of projects and business. It aims at helping you understand and appreciate complexity of Open Data, Open Source software and Open Access publications. It was specifically written for producers and users of environmental data, however, the guide will likely be useful to any data producers and user.

scholarly journals The 2017 Bioinformatics Open Source Conference (BOSC)

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1858
Author(s):  
Nomi L. Harris ◽  
Peter J.A. Cock ◽  
Brad Chapman ◽  
Christopher J. Fields ◽  
Karsten Hokamp ◽  
...  
Keyword(s):  
Software Development ◽  
Open Source ◽  
Open Source Software ◽  
Open Data ◽  
Open Science ◽  
Research Community ◽  
Biological Research ◽  
Non Profit ◽  
Bioinformatics Software ◽  
Bioinformatics Community

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC (http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

scholarly journals Cerebral Cortical Thickness Estimation using the TINA Open-Source Image Analysis Environment

2005 ◽  
Author(s):  
Marietta Scott ◽  
Paul A. Bromiley ◽  
Neil A. Thacker
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Cortical Thickness ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Magnetic Resonance Images ◽  
Source Image ◽  
Thickness Estimation ◽  
Analysis Environment

This paper gives an overview of the use and development of the TINA open-source medical image analysis environment, with respect to the determination of human cerebral cortical thickness estimation from magnetic resonance images. The ultimate aim of TINA is to provide a validated system where the source code and datasets are freely available in order to allow peer-validation of published results.

scholarly journals MatVTK - 3D Visualization for Matlab

2009 ◽  
Author(s):  
Erich Birngruber ◽  
René Donner ◽  
Georg Langs
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Medical Image ◽  
3D Visualization ◽  
Medical Image Analysis ◽  
Medical Data ◽  
Data Sets ◽  
Steep Learning Curve ◽  
Visualization Toolkit ◽  
Crucial Part

The rapid and flexible visualization of large amounts of com- plex data has become a crucial part in medical image analysis. In re- cent years the Visualization Toolkit (VTK) has evolved as the de-facto standard for open-source medical data visualization. It features a clean design based on a data flow paradigm, which the existing wrappers for VTK (Python, Tcl/Tk, Simulink) closely follow. This allows to elegantly model many types of algorithms, but presents a steep learning curve for beginners. In contrast to existing approaches we propose a framework for accessing VTK’s capabilities from within MATLAB, using a syntax which closely follows MATLAB’s graphics primitives. While providing users with the advanced, fast 3D visualization capabilities MATLAB does not provide, it is easy to learn while being flexible enough to allow for complex plots, large amounts of data and combinations of visualiza- tions. The proposed framework will be made available as open source with detailed documentation and example data sets.

scholarly journals I-DO: A Deformable Organisms framework for ITK

2006 ◽  
Author(s):  
Chris Mcintosh ◽  
Ghassan Hamarneh
Keyword(s):  
Spinal Cord ◽  
Image Analysis ◽  
Corpus Callosum ◽  
Artificial Life ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Open Science ◽  
Deformable Models ◽  
Control Mechanisms ◽  
High Level

Medical image analysis is an important problem relating to the study of various diseases. Since their inception to MICCAI in 2001, ‘’deformable organisms’’ have emerged as a fruitful methodology with examples ranging from 2D corpus callosum segmentation to 3D vasculature and spinal cord segmentation. Essentially we have developed an artificial life framework that complements classical deformable models (snakes and deformable meshes) with high-level, anatomically-driven control mechanisms. This paper describes the integration of deformable organisms into the Insight Toolkit (ITK) . Our code attempts to bridge the ITK framework and coding style with deformable organism design methodologies. In the interest of open science, as the framework develops it will serve as a basis for the community to develop new deformable organisms as well as experiment with those recently published by our group.

scholarly journals A value proposition for Open Science

2020 ◽  
Author(s):  
Jonathan Tennant
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Open Data ◽  
Open Science ◽  
Free Software ◽  
Turn Of The Millennium ◽  
Value Proposition ◽  
A Value ◽  
Human Understanding ◽  
Fundamental Freedoms

Open Science has become commonly understood in terms of its practices. Open Access, Open Data, and Open Source software are all becoming commonplace in academia. However, unlike the Free and Open Source Software movement, Open Science seems to have become largely divorced from its pluralistic philosophical and ethical foundations, which seem to have reignited from the humanities at the turn of the Millennium. To close this gap, I propose a new value-based proposition for Open Science, that is akin to the “four fundamental freedoms” of Richard Stallman that catalysed the Free Software movement. In doing so, I hope to provide a more common, unified, and human understanding to notions of openness in science.

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