MorFishJ is a software package that allows to perform a standardised, reproducible, and semi-automated traditional morphometric analysis of fishes from side-view images. Because ImageJ is commonly used by researchers to extract morphometric data from fish images, MorFishJ has been developed as an extension of this software and it can be used in both ImageJ 1.x and Fiji (ImageJ2) distribution.
First install ImageJ (instructions here) or Fiji (instructions here).
MorFishJ depends on ImageJ 1.53s, thus, if ImageJ/Fiji was previously installed, first check the current ImageJ version below the toolbar. If it is older than 1.53s, to update ImageJ click Help --> Update ImageJ..., choose the latest version and click OK. Then ImageJ/Fiji must be restarted.
To install MorFishJ:
- Download the latest release of
MorFishJfrom here as aZIPfile. - Extract the content.
- Copy the folder named
MorFishJin theImageJ/plugins/orFiji.app/plugins/directory.
Now MorFishJ is installed. Open ImageJ/FIJI and click Plugins --> MorFishJ --> MorFishJ GUI. The following GUI should appear in the upper left corner of the screen.
In Fiji it may be easier to use the Search field under the toolbar to find and start MorFishJ as the Plugins menu is often crowded.
Three morphometric analyses are currently available in MorFishJ:
- Main Traits: the workhorse of MorFishJ. Performs a complete morphometric analysis measuring 22 traits that cover all body parts visible from side view images, excluding dorsal, pelvic, and anal fins;
- Head Angles: allows to measure three head angles related to vision and feeding (Brandl and Bellwood 2013 Coral Reefs; Bellwood et al. 2014 Proc R Soc B: Biol Sci; Brandl et al. 2015 Proc R Soc B: Biol Sci);
- Gut Traits: allows to measure three intestinal traits related to fish diet (Ghilardi et al. 2021 Ecol Evol).
A step by step guide to the software can be found here.
Licensed under the MIT license.
To cite MorFishJ in publications use:
Mattia Ghilardi (2022). MorFishJ: A software package for fish traditional morphometrics. Zenodo. https://doi.org/10.5281/zenodo.6969273
A BibTeX entry for LaTeX users is:
@software{,
author = {Mattia Ghilardi},
title = {{MorFishJ: A software package for fish traditional
morphometrics}},
year = 2022,
publisher = {Zenodo},
doi = {10.5281/zenodo.6969273},
url = {https://doi.org/10.5281/zenodo.6969273}
}
Contributions are welcome. You can report bugs, ask questions or provide comments and feedback by filing an issue on Github here or writing to mattia.ghilardi91@gmail.com. You can also suggest additional analyses that could be useful to others researchers. These will be discussed and potentially implemented.