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| Hauptseite > Publikationsdatenbank > A Workflow for Polarized Light Imaging Using UNICORE Workflow Services > print |
| Hauptseite > Publikationsdatenbank > A Workflow for Polarized Light Imaging Using UNICORE Workflow Services > print |
| 001 | 185674 | ||
| 005 | 20210129214711.0 | ||
| 020 | _ | _ | |a 978-3-95806-004-3 |
| 037 | _ | _ | |a FZJ-2014-07099 |
| 100 | 1 | _ | |a Hagemeier, Björn |0 P:(DE-Juel1)132123 |b 0 |e Corresponding Author |u fzj |
| 111 | 2 | _ | |a UNICORE Summit 2014 |c Leipzig |d 2014-06-24 - 2014-06-24 |w Germany |
| 245 | _ | _ | |a A Workflow for Polarized Light Imaging Using UNICORE Workflow Services |
| 260 | _ | _ | |a Jülich |c 2014 |b Forschungszentrum Jülich GmbH Zentralbibliothek, Verlag |
| 295 | 1 | 0 | |a UNICORE Summit 2014 |
| 300 | _ | _ | |a 1-14 |
| 336 | 7 | _ | |a Contribution to a conference proceedings |b contrib |m contrib |0 PUB:(DE-HGF)8 |s 1418979816_21912 |2 PUB:(DE-HGF) |
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| 336 | 7 | _ | |a Conference Paper |0 33 |2 EndNote |
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| 336 | 7 | _ | |a INPROCEEDINGS |2 BibTeX |
| 490 | 0 | _ | |a IAS Series |v 26 |
| 520 | _ | _ | |a Understanding the anatomical structure of the human brain on the level of single nerve fibers is one of the most challenging tasks in neuroscience nowadays. In order to understand the connectivity of brain regions (affecting the brain function) on the one hand and to study neurodegenerative diseases on the other hand, a detailed three-dimensional map of nerve fibers has to be created. One technique applied to histological sections of postmortem brains is Polarized Light Imaging which allows the study of brain regions with a resolution at sub-millimeter scale. It is based on an optical property referred to as birefringence of myelin which surrounds the axons of nerve fibers. Therefore about 1500 slices, each 70 micron thick, of the post-mortem brain are imaged with a microscopic device using polarized light.The images of brain slices are processed with a chain of tools for calibration, independent component analysis, enhanced analysis, stitching and segmentation. These tools have been integrated in a UNICORE workflow, exploiting many of the workflow system features, such as control structures and human interaction. Prior to the introduction of the UNICORE workflow system, the tools involved were run manually by their respective developers. Thus, once one step in the process was finished, the developer of the next tool in the chain would retrieve the data and run his tools on the output of the former. This manual approach led to delays in the entire process.The introduction of the UNICORE workflow system for this particular use case resulted in several benefits. First of all, the results are easier to reproduce now, as fewer manual steps are involved. Secondly, the makespan of the entire workflow could be reduced to hours rather than weeks, because of the almost fully automated workflow. Lastly, only the automated approach will allow for the timely analysis of a large number of brain slices that are expected to be available in the near future.This workflow is interesting from the technical point of view, as it takes UNICORE and its workflow system to the limits. Workarounds were required for some peculiarities of the workflow system. For example, in order to use results of one workflow job as input in the next job, the workflow system usually copies this data to the central workflow storage before copying it into the working directory of the next job. The amount of data for a single brain slice is on the order of magnitude of up to 1TB, with intermediate results at the same scale. Thus, the total amount of data easily adds up to several TB of data movement within the workflow, which can and should be avoided.This paper will describe the situation as of version 6.6.0 of the workflow system. Results of this work have been incorporated in subsequent versions starting with 7.0.0. However, some of the approaches for processing large sets of data used here will still apply in future versions of the UNICORE system. |
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| 856 | 4 | _ | |u https://juser.fz-juelich.de/record/185544/files/FZJ-2014-06971.pdf |
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