The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed).

What FishInspector can do for you


FishInspector v1.03 screenshotScreenshot of FishInspector Software Version 1.03

The FishInspector software allows the user-friendly and easy annotation of features in zebrafish embryo 2-dimensional images. Features are detected automatically but may require correction by the user (implemented in the software). At present only lateral images can be analysed, but the software could be extended to analyse dorsoventral images as well. The software has been initially developed for images obtained with an automated capillary position system. However, images from other sources can be used as well after appropriate conversion (see here). During the installation process an appropriate version of MATLAB runtime will be installed as well. No full MATLAB installation is required. FishInspector has been tested on Windows 7 but may run on other Windows versions as well.

More details on the software and the subsequent data analysis can be found in the following publication:

Teixido, E., Kießling, T.R., Krupp, E., Quevedo, C., Muriana, A., and Scholz, S. (2019): Automated morphological feature assessment for zebrafish embryo developmental toxicity screens. Tox. Sci. 167(2), 438–449

Plugins, future versions

The software is intended to be modified and extended by the community. If you are interested or have a special interest please do not hesitate to contact us.

Logo of FishInspector
Programming language
  • MATLAB 100%
  • GPL-3.0-or-later
</>Source code

Participating organisations

Helmholtz Centre for Environmental Research (UFZ)