The MorFishJ User Manual

MorFishJ v0.2.2

Author

Mattia Ghilardi

Published

October 30, 2023

Introduction

MorFishJ is an open-source software package for traditional morphometric analysis of fish in ImageJ. With MorFishJ you can collect morphological trait data from fish images in a standardised and reproducible way through a semi-automated procedure, which accelerates data collection and increases data accuracy by reducing user bias.

Motivation

While advances in modern morphometrics (landmarks configuration and outline analysis) have increasingly facilitated data acquisition and analysis, traditional morphometrics has not kept pace. Collection of traditional morphometric data from fish images is generally slow and not reproducible. A typical workflow in ImageJ is:

  1. Open an image.
  2. Adjust the image if necessary (or do this beforehand with another software).
  3. Draw reference lines to help with trait measurement (Optional).
  4. Measure traits one by one.
  5. Save results.
  6. Close the image (losing track of the work done).
  7. Open the next image and repeat the procedure.

Additionally, traits are often defined and measured differently by different researchers as a standardised protocol does not exist yet, making it impractical to merge data obtained from multiple studies.

The MorFishJ package

MorFishJ allows users to perform a complete morphometric characterisation in a limited time while recording and storing all steps, and saving results in a ready-to-use format suitable for statistical analysis with multiple software. Analyses of large photographic databases are facilitated by allowing users to stop and restart their analyses without losing progress.

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}
}

About this manual

This manual is a step-by-step user guide to MorFishJ. It explains best practices for project organisation, walks through each implemented analysis, and provides detailed explanations and examples for specific steps.

Versioning

The manual follows the same versioning of MorFishJ. For each new release of MorFishJ this manual will be updated and will be given the same version number.

The latest version of the manual can always be accessed at https://mattiaghilardi.github.io/MorFishJ_manual/.

Previous versions can be accessed at:

A list of changes made for each version of MorFishJ can be seen here.