Published April 24, 2019 | Version v1
Dataset Open

3dpf zebrafish larvae, 96 well plate,Tg(wt1b:EGFP), dorsal view, ACQUIFER Imaging Machine

  • 1. ACQUIFER is a division of DITABIS AG, Pforzheim, Germany


Datasets originate from internal test runs at ACQUIFER on the Imaging Machine (see also application note on "The ACQUIFER PlateViewer: A tool for visualizing high content screening data and supervised feedback microscopy")

The datasets contain images acquired from 96 Tg(wt1b:EGFP) embryos at 3 dpf aligned in agarose cavities generated with 3d printed orientation tools (Wittbrodt, Jonas N., Urban Liebel, and Jochen Gehrig. "Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing." BMC biotechnology 14.1 (2014): 36.):

- 2x, 4x, 10x views

- for each well (e.g. A001) a multi-color z-stack was acquired, with  N z-slices (SLNNN) in two channels: BF (CO6) and GFP (CO3)

Example file name containing metadata: -A001--PO01--LO001--CO3--SL001--PX32500--PW0100--IN0100--TM281--X014580--Y011262--Z210710--T0200256066--WE00001.tif

Used also as benchmark dataset for Multi-Template Matching by Thomas, LSV and Gehrig, J

See implementation in Fiji

and in KNIME


j.gehrig(at), l.thomas(at)


Ethic statement

The work presented does not involve work with animals according to German and European
legislation. All experiments have been performed at stages prior to the legal onset of animal life.
To obtain zebrafish embryos and larvae, fish were maintained in closed stocks at Heidelberg University.
Zebrafish husbandry and experiments are under the institutional control of the Universities animal
welfare agency. All the zebrafish husbandry and experimental procedures were performed in
accordance with the German animal welfare standards (Tierschutzgesetz §11, Abs. 1, Nr. 1, husbandry
permit number 35-9185.64/BH Wittbrodt) and in accordance with German and European Union animal
welfare guidelines. The fish facility is under the supervision of the local representative of the animal
welfare agency.


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Additional details

Related works

Is supplement to
Journal article: 10.1186/s12859-020-3363-7 (DOI)
Journal article: 10.1186/1472-6750-14-36 (DOI)