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Current Directions in Biomedical Engineering

Joint Journal of the German Society for Biomedical Engineering in VDE and the Austrian and Swiss Societies for Biomedical Engineering

Editor-in-Chief: Dössel, Olaf

Editorial Board: Augat, Peter / Buzug, Thorsten M. / Haueisen, Jens / Jockenhoevel, Stefan / Knaup-Gregori, Petra / Kraft, Marc / Lenarz, Thomas / Leonhardt, Steffen / Malberg, Hagen / Penzel, Thomas / Plank, Gernot / Radermacher, Klaus M. / Schkommodau, Erik / Stieglitz, Thomas / Urban, Gerald A.


CiteScore 2018: 0.47

Source Normalized Impact per Paper (SNIP) 2018: 0.377

Open Access
Online
ISSN
2364-5504
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ZebrafishMiner: an open source software for interactive evaluation of domain-specific fluorescence in zebrafish

Markus Reischl
  • Corresponding author
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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  • Other articles by this author:
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/ Andreas Bartschat
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
  • Other articles by this author:
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/ Urban Liebel / Jochen Gehrig
  • ACQUIFER, Division of DITABIS, Digital Biomedical Imaging Systems AG, 75179 Pforzheim, Germany
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/ Ference Müller
  • Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, United Kingdom
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/ Ralf Mikut
  • Institute for Applied Computer Science, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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Published Online: 2017-09-07 | DOI: https://doi.org/10.1515/cdbme-2017-0042

Abstract

High-throughput microscopy makes it possible to observe the morphology of zebrafish on large scale to quantify genetic, toxic or drug effects. The image acquisition is done by automated microscopy, images are evaluated automatically by image processing pipelines, tailored specifically to the requirements of the scientific question. The transfer of such algorithms to other projects, however, is complex due to missing guidelines and lack of mathematical or programming knowledge. In this work, we implement an image processing pipeline for automatic fluorescence quantification in user-defined domains of zebrafish embryos and larvae of different age. The pipeline is capable of detecting embryos and larvae in image stacks and quantifying domain activity. To make this protocol available to the community, we developed an open source software package called „ZebrafishMiner“ which guides the user through all steps of the processing pipeline and makes the algorithms available and easy to handle. We implemented all routines in an MATLAB-based graphical user interface (GUI) that gives the user control over all image processing parameters. The software is shipped with a manual of 30 pages and three tutorial datasets, which guide the user through the manual step by step. It can be downloaded at https://sourceforge.net/projects/scixminer/.

Keywords: high throughput; zebrafish; image processing

About the article

Published Online: 2017-09-07


Citation Information: Current Directions in Biomedical Engineering, Volume 3, Issue 2, Pages 199–202, ISSN (Online) 2364-5504, DOI: https://doi.org/10.1515/cdbme-2017-0042.

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©2017 Markus Reischl et al., published by De Gruyter. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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