https://github.com/jcmontesherrera/jcmh-phd-thesis-notebooks

Notebooks and scripts created during the course of PhD research chapters.

https://github.com/jcmontesherrera/jcmh-phd-thesis-notebooks

Repository

Notebooks and scripts created during the course of PhD research chapters.

https://github.com/jcmontesherrera/JCMH-phd-thesis-notebooks/blob/main/

# JCMH-PhD-Thesis-notebooks
Notebooks and scripts created during the course of PhD research chapters.


## How to cite
- Montes-Herrera, J.C. 2023. Benthic biologist's digital field log: Notebooks for biodiversity mapping with structure-from-motion photogrammetry and hyperspectral imaging. (Version v1.1.1) [Computer software]
## Contact
J.C. Montes-Herrera
juancarlos.montesherrera@utas.edu.au


## Geographic coverage
- Ellis Fjord, Vestfold Hills, Antarctica
- McMurdo Sound, Ross Sea, Antarctica
- Fossil Cove, Derwent estuary, Tasmania, AU

## Taxonomic coverage
- Serpulid polychaete reefs and associated communities
- Antarctic lithogenic crustose coralline algae (CCA)
- Tasmania zoogenic CCA

## Keywords
sfm-photogrammetry, imaging-spectroscopy, hyperspectral-imaging, underwater-hyperspectral-imaging, python, jupyter

## Project Data or Deliverables
- Python Jupyter notebooks for image processing and analysis

## Publications
- Montes-Herrera, J. C., Cimoli, E., Cummings, V., Hill, N., Lucieer, A., Lucieer, V. 2021. Underwater Hyperspectral Imaging (UHI): A Review of Systems and Applications for Proximal Seafloor Ecosystem Studies. Remote Sensing. 13 (17), 3451. https://doi.org/10.3390/rs13173451

- Montes-Herrera, J.C., Hill, N., Cummings, V.J., Johnstone, G., Stark, J.S., Lucieer, V. (accepted). Remote sensing of Antarctic polychaete reefs: Reproducible workflows for quantifying benthic structural complexity with action cameras, remotely operated vehicles, and structure-from-motion photogrammetry. *Remote Sensing in Ecology and Conservation*

- Montes-Herrera, J. C., Cimoli, E., Cummings, V., Nelson, W., Hill, N., Lucieer, A., Lucieer, V. (in review). Hyperspectral imaging to quantify thalli R-Phycoerythrin: A case study on two phenotypes of Antarctic crustose coralline algae (Tethysphytum antarcticum). *Journal of Phycology*.

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