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A software package for fish traditional morphometric analysis from side view images

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License DOI Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub release (latest by date)

MorFishJ


Description

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.

Installation

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:

  1. Download the latest release of MorFishJ from here as a ZIP file.
  2. Extract the content.
  3. Copy the folder named MorFishJ in the ImageJ/plugins/ or Fiji.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.

Available analyses

Three morphometric analyses are currently available in MorFishJ:

User manual

A step by step guide to the software can be found here.

Licenses

Licensed under the MIT license.

Citation

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}
}

Contributing

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.