Description
Foraminiferal Image Analysis and Test Measurement.
Description
The goal of this collection of functions is to provide an easy to use tool for the measurement of foraminifera and other unicellulars organisms size. With functions developed to guide foraminiferal test biovolume calculations and cell biomass estimations. The volume function includes several microalgae models geometric adaptations based on Hillebrand et al. (1999) <doi:10.1046/j.1529-8817.1999.3520403.x>, Sun and Liu (2003) <doi:10.1093/plankt/fbg096> and Vadrucci, Cabrini and Basset (2007) <doi:10.1285/i1825229Xv1n2p83>.
README.md
forImage
The goal of forImage is to facilitate foraminiferal test measurement and biomass estimation.
The package is proposed as an alternative to manual and/or multi-software dependent methods for biometry and biomass estimation.
Installation
The package requires Python >= 3.5.
You can install forImage from github with:
remotes::install_github("ThaiseRF/forImage", build_vignettes = TRUE)
# Using `build_vignettes = TRUE` will slow down the install, but is necessary if
# you want to read the vignette, which is recommended
Use install_measure() to install all Python modules dependencies (scipy, imutils, numpy, pandas, Pillow and OpenCV) at once in a virtual environment. This function is a wrapper of reticulate py_install() and requires a conda installation on Windows.
To install the Python modules via pip on Ubuntu:
sudo apt-get install python-pip
sudo pip install pip --upgrade
sudo pip install scipy
On Windows:
python -m pip install --upgrade pip
pip install scipy
On macOs:
python3 -m pip install --upgrade pip
pip3 install scipy