{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,23]],"date-time":"2025-09-23T14:28:51Z","timestamp":1758637731261},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: To reliably assess the effects of unknown chemicals on the development of fluorescently labeled sensory-, moto- and interneuron populations in the spinal cord of zebrafish, automated data analysis is essential.<\/jats:p>\n               <jats:p>Results: For the evaluation of a high-throughput screen of a large chemical library, we developed a new method for the automated extraction of quantitative information from green fluorescent protein (eGFP) and red fluorescent protein (RFP) labeled spinal cord neurons in double-transgenic zebrafish embryos. The methodology comprises region of interest detection, intensity profiling with reference comparison and neuron distribution histograms. All methods were validated on a manually evaluated pilot study using a Notch inhibitor dose-response experiment. The automated evaluation showed superior performance to manual investigation regarding time consumption, information detail and reproducibility.<\/jats:p>\n               <jats:p>Availability and implementation: Being part of GNU General Public Licence (GNU-GPL) licensed open-source MATLAB toolbox Gait-CAD, an implementation of the presented methods is publicly available for download at http:\/\/sourceforge.net\/projects\/zebrafishimage\/.<\/jats:p>\n               <jats:p>Contact: \u00a0johannes.stegmaier@kit.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt600","type":"journal-article","created":{"date-parts":[[2013,10,18]],"date-time":"2013-10-18T02:15:04Z","timestamp":1382062504000},"page":"726-733","source":"Crossref","is-referenced-by-count":5,"title":["Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish"],"prefix":"10.1093","volume":"30","author":[{"given":"Johannes","family":"Stegmaier","sequence":"first","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]},{"given":"Maryam","family":"Shahid","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"},{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]},{"given":"Masanari","family":"Takamiya","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]},{"given":"Lixin","family":"Yang","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]},{"given":"Sepand","family":"Rastegar","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]},{"given":"Markus","family":"Reischl","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]},{"given":"Uwe","family":"Str\u00e4hle","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"},{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]},{"given":"Ralf","family":"Mikut","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, 2Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and 3Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2013,10,17]]},"reference":[{"key":"2023012710425906800_btt600-B1","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1109\/TBME.2009.2035102","article-title":"Improved automatic detection and segmentation of cell nuclei 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