A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing Pipelines
Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by...
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doaj-4ebf30e2573c4265a7ba12147dc7a5252020-11-24T23:59:33ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962013-12-01710.3389/fninf.2013.0004674124A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing PipelinesMichael eGrauer0Patrick eReynolds1Marion eHoogstoel2Francois eBudin3Martin Andreas Styner4Ipek eOguz5Kitware Inc.Kitware Inc.University of North CarolinaUniversity of North CarolinaUniversity of North CarolinaUniversity of IowaImage processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based UI, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline.http://journal.frontiersin.org/Journal/10.3389/fninf.2013.00046/fullMRIbrain image processingautomated pipelinesrodent imagingworkflow processing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Michael eGrauer Patrick eReynolds Marion eHoogstoel Francois eBudin Martin Andreas Styner Ipek eOguz |
spellingShingle |
Michael eGrauer Patrick eReynolds Marion eHoogstoel Francois eBudin Martin Andreas Styner Ipek eOguz A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing Pipelines Frontiers in Neuroinformatics MRI brain image processing automated pipelines rodent imaging workflow processing |
author_facet |
Michael eGrauer Patrick eReynolds Marion eHoogstoel Francois eBudin Martin Andreas Styner Ipek eOguz |
author_sort |
Michael eGrauer |
title |
A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing Pipelines |
title_short |
A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing Pipelines |
title_full |
A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing Pipelines |
title_fullStr |
A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing Pipelines |
title_full_unstemmed |
A Midas Plugin to Enable Construction of Reproducible Web-based Image Processing Pipelines |
title_sort |
midas plugin to enable construction of reproducible web-based image processing pipelines |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Neuroinformatics |
issn |
1662-5196 |
publishDate |
2013-12-01 |
description |
Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based UI, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline. |
topic |
MRI brain image processing automated pipelines rodent imaging workflow processing |
url |
http://journal.frontiersin.org/Journal/10.3389/fninf.2013.00046/full |
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