scholarly journals Karawun: assisting evaluation of advances in multimodal imaging for neurosurgical planning and intraoperative neuronavigation

2021 ◽  
Author(s):  
Richard Beare ◽  
Bonnie Alexander ◽  
Aaron Warren ◽  
Michael Kean ◽  
Marc Seal ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Image Guidance ◽  
Image Data ◽  
Software Tool ◽  
Neurosurgical Planning ◽  
Wide Range ◽  
Imaging Research ◽  
The Impact ◽  
Integrate Research

AbstractSubmitted to Magnetic Resonance in MedicinePurposeTo introduce a tool allowing neurosurgeons to evaluate the results of research tractography workflows for presurgical planning and intraoperative image-guidance, using standard neurosurgical navigation platforms.Theory and MethodsImproving communication between neurosurgeons and researchers developing new image acquisition and processing methods is critical for rapid translation of research to surgical practice. Presenting research outputs within existing clinical workflows is one approach that can assist such interdisciplinary communication. Neurosurgical navigation platforms can display and manipulate a wide range of medical image data and associated delineations and thus allow clinicians to evaluate the impact of new imaging research on their work. Currently, it is extremely difficult to integrate research-based image processing outputs into standard neurosurgical navigation platforms.ResultsIn this note we introduce Karawun, an open-source software tool for converting outputs from research imaging pipelines, especially diffusion MRI tractography reconstructions using advanced methodologies currently unavailable on commercial navigation platforms, into forms that can be imported into the Brainlab neurosurgical navigation platform (Brainlab AG, Munich, Germany). The externally created tractography images and delineations can be viewed and manipulated as if they were created by Brainlab. We illustrate how two surgical workups, created using open-source tools and different processing choices can be presented to the neurosurgeon who can evaluate the impact of the differences between the two workups on surgical decisions.ConclusionKarawun allows researchers developing novel imaging methodologies to display their results in environments that are familiar to clinical end-users, especially neurosurgeons, thus assisting translation of research into clinical practice.

Developer Centrality and the Impact of Value Congruence and Incongruence on Commitment and Code Contribution Activity in Open Source Software Communities

MIS Quarterly ◽  
2019 ◽  
Vol 43 (3) ◽  
pp. 951-976
Author(s):  
Likoebe M. Maruping ◽  
◽  
Sherae L. Daniel ◽  
Marcelo Cataldo ◽  
◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Value Congruence ◽  
The Impact

scholarly journals MCR: Open-Source Software to Automate Compilation of Health Study Report-Back

2021 ◽  
Vol 18 (11) ◽  
pp. 6104
Author(s):  
Erin Polka ◽  
Ellen Childs ◽  
Alexa Friedman ◽  
Kathryn S. Tomsho ◽  
Birgit Claus Henn ◽  
...  
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Open Source Software ◽  
Research Team ◽  
Self Determination ◽  
Health Study ◽  
Equitable Access ◽  
Team Members ◽  
Study Participants ◽  
The Impact

Sharing individualized results with health study participants, a practice we and others refer to as “report-back,” ensures participant access to exposure and health information and may promote health equity. However, the practice of report-back and the content shared is often limited by the time-intensive process of personalizing reports. Software tools that automate creation of individualized reports have been built for specific studies, but are largely not open-source or broadly modifiable. We created an open-source and generalizable tool, called the Macro for the Compilation of Report-backs (MCR), to automate compilation of health study reports. We piloted MCR in two environmental exposure studies in Massachusetts, USA, and interviewed research team members (n = 7) about the impact of MCR on the report-back process. Researchers using MCR created more detailed reports than during manual report-back, including more individualized numerical, text, and graphical results. Using MCR, researchers saved time producing draft and final reports. Researchers also reported feeling more creative in the design process and more confident in report-back quality control. While MCR does not expedite the entire report-back process, we hope that this open-source tool reduces the barriers to personalizing health study reports, promotes more equitable access to individualized data, and advances self-determination among participants.

scholarly journals Knowledge sharing in open source software communities: motivations and management

2015 ◽  
Vol 19 (4) ◽  
pp. 791-813 ◽  
Author(s):  
Zilia Iskoujina ◽  
Joanne Roberts
Keyword(s):  
Knowledge Sharing ◽  
Open Source ◽  
Open Source Software ◽  
Online Communities ◽  
Descriptive Analysis ◽  
Online Questionnaire ◽  
Content Type ◽  
The Individual ◽  
The Impact

Purpose – This paper aims to add to the understanding of knowledge sharing in online communities through an investigation of the relationship between individual participant’s motivations and management in open source software (OSS) communities. Drawing on a review of literature concerning knowledge sharing in organisations, the factors that motivate participants to share their knowledge in OSS communities, and the management of such communities, it is hypothesised that the quality of management influences the extent to which the motivations of members actually result in knowledge sharing. Design/methodology/approach – To test the hypothesis, quantitative data were collected through an online questionnaire survey of OSS web developers with the aim of gathering respondents’ opinions concerning knowledge sharing, motivations to share knowledge and satisfaction with the management of OSS projects. Factor analysis, descriptive analysis, correlation analysis and regression analysis were used to explore the survey data. Findings – The analysis of the data reveals that the individual participant’s satisfaction with the management of an OSS project is an important factor influencing the extent of their personal contribution to a community. Originality/value – Little attention has been devoted to understanding the impact of management in OSS communities. Focused on OSS developers specialising in web development, the findings of this paper offer an important original contribution to understanding the connections between individual members’ satisfaction with management and their motivations to contribute to an OSS project. The findings reveal that motivations to share knowledge in online communities are influenced by the quality of management. Consequently, the findings suggest that appropriate management can enhance knowledge sharing in OSS projects and online communities, and organisations more generally.

MITK Diffusion Imaging

2012 ◽  
Vol 51 (05) ◽  
pp. 441-448 ◽  
Author(s):  
P. F. Neher ◽  
I. Reicht ◽  
T. van Bruggen ◽  
C. Goch ◽  
M. Reisert ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
High Performance ◽  
Diffusion Imaging ◽  
Software Tool ◽  
Brain Anatomy ◽  
Sustainable Evaluation ◽  
Imaging Research ◽  
Interactive Data

SummaryBackground: Diffusion-MRI provides a unique window on brain anatomy and insights into aspects of tissue structure in living humans that could not be studied previously. There is a major effort in this rapidly evolving field of research to develop the algorithmic tools necessary to cope with the complexity of the datasets.Objectives: This work illustrates our strategy that encompasses the development of a modularized and open software tool for data processing, visualization and interactive exploration in diffusion imaging research and aims at reinforcing sustainable evaluation and progress in the field.Methods: In this paper, the usability and capabilities of a new application and toolkit component of the Medical Imaging and Interaction Toolkit (MITK, www.mitk.org), MITKDI, are demonstrated using in-vivo datasets.Results: MITK-DI provides a comprehensive software framework for high-performance data processing, analysis and interactive data exploration, which is designed in a modular, extensible fashion (using CTK) and in adherence to widely accepted coding standards (e.g. ITK, VTK). MITK-DI is available both as an open source software development toolkit and as a ready-to-use in stallable application.Conclusions: The open source release of the modular MITK-DI tools will increase verifiability and comparability within the research community and will also be an important step towards bringing many of the current techniques towards clinical application.

scholarly journals What can scholars learn from Open Source software communities during pandemics

2020 ◽  
Author(s):  
Jonathan Tennant ◽  
Tom Crick
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Scholarly Communication ◽  
Social Demand ◽  
Research Communities ◽  
The Social ◽  
Current Outbreak ◽  
The Impact ◽  
Global Research

When the SARS-CoV-2 outbreak began on January 31, 2020, no-one could have anticipated the impact that it would have on our scholarly communication and publishing systems. That is, perhaps, unless you work on open source software. Right now, global research communities are united to collaborate on solving the threat of the pandemic, sharing resources and knowledge more efficiently and effective than ever before, a process broadly described as ‘open scholarship’ (Dunleavy, 2020). This is essentially akin to how free and open source software (FOSS) communities have been operating now for decades (Willinsky, 2005). Recently, we participated in a “massively open online paper”, or MOOP, that explored the intersections between FOSS and open scholarship (Tennant, Agarwal, et al., 2020). Here, we want to summarise our key findings from that project, and place them in the context of the current outbreak. Critically, this pandemic shows us that many of the pervasive and systemic issues surrounding the evaluation, valuation, use and operationalisation of “openness” in scholarship can be extremely easily bypassed when the social demand and urgency is there, thus showing that the primary barriers towards open scholarship are inherently political and not technical.

scholarly journals Cantera: an open source software tool for integrating complex thermo-chemistry into device-level simulations

2020 ◽  
Author(s):  
Richard West ◽  
Robert Kee ◽  
Kyle Niemeyer ◽  
Steven C. DeCaluwe ◽  
C. Goldsmith ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tool

scholarly journals An uncertainty-based protocol for the setup and measurement of soot/black carbon emissions from gas flares using sky-LOSA

2020 ◽  
Author(s):  
Bradley M. Conrad ◽  
Matthew R. Johnson
Keyword(s):  
Open Source ◽  
Black Carbon ◽  
Open Source Software ◽  
Carbon Emissions ◽  
Climate Models ◽  
Optical Measurement ◽  
Measurement Data ◽  
Software Tool ◽  
Measurement Protocol ◽  
Measurement Uncertainties

Abstract. Gas flaring is an important source of atmospheric soot/black carbon, especially in sensitive Arctic regions. However, emissions have traditionally been challenging to measure and remain poorly characterized, confounding international reporting requirements and adding uncertainty to climate models. The sky-LOSA optical measurement technique has emerged as a powerful means to quantify flare black carbon emissions in the field, but broader adoption has been hampered by the complexity of its deployment, where decisions during setup in the field can have profound, non-linear impacts on achievable measurement uncertainties. To address this challenge, this paper presents a prescriptive measurement protocol and associated open-source software tool that simplifies acquisition of sky-LOSA data in the field. Leveraging a comprehensive Monte Carlo-based General Uncertainty Analysis (GUA) to predict measurement uncertainties over the entire breadth of possible measurement conditions, general heuristics are identified to guide a sky-LOSA user toward optimal data collection. These are further extended in the open-source software utility, SetupSkyLOSA, which interprets the GUA results to provide detailed guidance for any specific combination of location, date/time, and flare, plume, and ambient conditions. Finally, a case study of a sky-LOSA measurement at an oil and gas facility in Mexico is used to demonstrate the utility of the software tool, where potentially small region(s) of optimal instrument setup are easily and quickly identified. It is hoped that this work will help increase the accessibility of the sky-LOSA technique and ultimately the availability of field measurement data for flare black carbon emissions.

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