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CollatriX 2.0

User-Friendly Photogrammetry Software

Read the Manual »

Report Bug . Request Feature

DOI DOI Downloads Contributors Stargazers Issues License

Table Of Contents

About The Project

The path from measuring an image to having a clean dataset of measurements can often be complicated. CollatriX was designed to help.

This all started with the simple need for a tool to collate the csv outputs from MorphoMetriX into one large single data frame containing the image, animal ID, measurements, and notes.

But calculating accurate measurements requires more. CollatriX V2 now has several additional tools to bring in altitude measurements from a laser altimter by helping accurately correct timestamps and merge datasets.

CollatriX can also calcuate several body condition metrics for cetaceans.

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Getting Started

To install CollatriX as an application go to our releases page and download the dmg (for macs) or exe (for windows). Check out the manual for more detail.

Note IF you are using a mac - you’ll also need exiftool installed. If you already have it installed, great! If not, download the zipfile here for an easy download

Usage

Please read our manual and check out our tutorial videos for detailed instructions.

Attribution

If you use this software please cite our paper:
Bird C.N. & Bierlich K.C., (2020). CollatriX: A GUI to collate MorphoMetriX outputs. Journal of Open Source Software, 5(51), 2328, https://doi.org/10.21105/joss.02328

Additionally:

  • if you calculate Body Volume cite:

    • Circular frustums: Christiansen, F., Vivier, F., Charlton, C., Ward, R., Amerson, A., Burnell, S., & Bejder, L. Maternal body size and condition determine calf growth rates in southern right whales (2018). Maternal body size and condition determine calf growth rates in southern right whales. Marine Ecology Progress Series, 592, 267–281. http://doi.org/10.3354/meps12522

    • Elliptical: Christiansen F,  Sironi M,  Moore MJ, et al.  Estimating body mass of free-living whales using aerial photogrammetry and 3D volumetrics. Methods Ecol Evol.  2019; 10: 2034–2044. https://doi.org/10.1111/2041-210X.13298

  • if you calucalte BAI cite: Burnett, Jonathan D., Leila Lemos, Dawn Barlow, Michael G. Wing, Todd Chandler, and Leigh G. Torres. 2018. “Estimating Morphometric Attributes of Baleen Whales with Photogrammetry from Small UASs: A Case Study with Blue and Gray Whales.” Marine Mammal Science 35 (1): 108–39. https://doi.org/10.1111/mms.12527.

Contributing

We designed CollatriX with future collaborations in mind and we'd love for you to contribute! If you'd like to contribute please see our contributing guidelines

Creating A Pull Request

  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request

License

Copyright (c) 2020 Clara Bird, KC Bierlich

Collatrix is free software made available under the MIT License. For details see the the LICENSE file.

Authors

  • Clara N. Bird - Researcher, PhD Wildlife Science - Clara Bird
  • KC Bierlich - Assistant Professor Senior Research, PhD Marine Science and Conservation - KC Bierlich