ZebrafishMiner: An open source software for interactive evaluation of domain-specific fluorescence in zebrafish

Markus Reischl*, Andreas Bartschat, Urban Liebel, Jochen Gehrig, Ference Müller, Ralf Mikut

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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/.

Original languageEnglish
Pages (from-to)199-202
Number of pages4
JournalCurrent Directions in Biomedical Engineering
Issue number2
Publication statusPublished - Sept 2017

Bibliographical note

Funding Information:
Research funding: We would like to express our gratitude to DAAD, BIF-IGS and Helmholtz Association for funding and supporting this research work. Conflict of interest: Authors state no conflict of interest. Informed consent: Informed consent is not applicable. Ethical approval: The conducted research is not related to either human or animals use.

Publisher Copyright:
© 2017 Markus Reischl et al., published by De Gruyter.


  • High throughput
  • Image processing
  • Zebrafish

ASJC Scopus subject areas

  • Biomedical Engineering


Dive into the research topics of 'ZebrafishMiner: An open source software for interactive evaluation of domain-specific fluorescence in zebrafish'. Together they form a unique fingerprint.

Cite this