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2 results for “ACQUIFER”
102 hpf medaka embryos in 96 well plate (4 embryo/well) - brightfield - 2X magnification - ACQUIFER Imaging Machine
<p>Dataset originates from:</p> <p>Gierten, J., Pylatiuk, C., Hammouda, O. T., Schock, C., Stegmaier, J., Wittbrodt, J., Gehrig, J. and Loosli, F. (2020). <strong>Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions</strong>. Sci Rep <em>10</em>, 2046, doi:<a href="https://doi.org/10.1038/s41598-020-58563-w">10.1038/s41598-020-58563-w</a>.</p> <p>Used as benchmark dataset for Multi-Template-Matching by Thomas and Gehrig </p> <p>See implementation in Fiji <a href="https://github.com/LauLauThom/MultipleTemplateMatching">https://github.com/LauLauThom/MultipleTemplateMatching</a></p> <p>and in KNIME <a href="https://github.com/LauLauThom/MultipleTemplateMatching-KNIME">https://github.com/LauLauThom/MultipleTemplateMatching-KNIME</a></p> <p>Contacts: j.gehrig(at)acquifer.de, l.thomas(at)acquifer.de, jakob.gierten(at)cos.uni-heidelberg.de</p>
3dpf zebrafish larvae, 96 well plate,Tg(wt1b:EGFP), dorsal view, ACQUIFER Imaging Machine
<p>Datasets originate from internal test runs at ACQUIFER on the Imaging Machine (see also application note on "<a href="https://www.acquifer.de/downloads/Clicktoolappnote_ImagingMachine.pdf">The ACQUIFER PlateViewer: A tool for visualizing high content screening data and supervised feedback microscopy</a>")</p> <p>The datasets contain images acquired from 96 <em>Tg(wt1b:EGFP)</em> embryos at 3 dpf aligned in agarose cavities generated with 3d printed orientation tools (<a href="https://rdcu.be/byto9">Wittbrodt, Jonas N., Urban Liebel, and Jochen Gehrig. "Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing." <em>BMC biotechnology</em> 14.1 (2014): 36.</a>):</p> <p>- 2x, 4x, 10x views</p> <p>- for each well (e.g. <em>A001</em>) a multi-color z-stack was acquired, with N z-slices (SL<em>NNN</em>) in two channels: BF (CO<em>6</em>) and GFP (CO<em>3</em>)</p> <p>Example file name containing metadata: -<strong><em>A001-</em></strong>-PO01--LO001--<em><strong>CO3</strong></em>--<em><strong>SL001</strong></em>--PX32500--PW0100--IN0100--TM281--X014580--Y011262--Z210710--T0200256066--WE00001.tif</p> <p>Used also as benchmark dataset for Multi-Template Matching by Thomas, LSV and Gehrig, J</p> <p>See implementation in Fiji <a href="https://github.com/LauLauThom/MultipleTemplateMatching">https://github.com/LauLauThom/MultipleTemplateMatching</a></p> <p>and in KNIME <a href="https://github.com/LauLauThom/MultipleTemplateMatching-KNIME">https://github.com/LauLauThom/MultipleTemplateMatching-KNIME</a></p> <p>Contact:</p> <p>j.gehrig(at)acquifer.de, l.thomas(at)acquifer.de</p> <p> </p> <p><strong>Ethic statement</strong></p> <p>The work presented does not involve work with animals according to German and European<br> legislation. All experiments have been performed at stages prior to the legal onset of animal life.<br> To obtain zebrafish embryos and larvae, fish were maintained in closed stocks at Heidelberg University.<br> Zebrafish husbandry and experiments are under the institutional control of the Universities animal<br> welfare agency. All the zebrafish husbandry and experimental procedures were performed in<br> accordance with the German animal welfare standards (Tierschutzgesetz §11, Abs. 1, Nr. 1, husbandry<br> permit number 35-9185.64/BH Wittbrodt) and in accordance with German and European Union animal<br> welfare guidelines. The fish facility is under the supervision of the local representative of the animal<br> welfare agency.</p>
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