Plankton Toolbox

The Plankton Toolbox is a free tool for aquatic scientists, and others, working with environmental monitoring related to phyto- and zooplankton.

Features

• Counting module for use by the microscope
• Imports phyto- or zooplankton data in .txt and .xlsx files in different formats (configurable)
• Work with data on abundance, biovolume and carbon content
• Data screening - quality control of data (in early development)
• Report generator
• Aggregate data, e.g. from species level to class level
• Plotting tools
• Statistics (in early development)
• Export data in .txt or .xlsx for further analysis or plotting

Documentation

Documentation is available here:

• Introduction
• User guide
• Datasets and parsers
• Species lists, etc.

Downloads

The latest version of Plankton Toolbox is available for MacOS and Windows at: http://nordicmicroalgae.org/tools

Screenshot

Installation

Installation is not needed for users who uses the pre-build executables for Windows or Mac. Linux users must install the software by following the instruction below.

For development the same installation process can be used. Executables can be generated by using "pyinstaller".

git clone https://github.com/planktontoolbox/plankton-toolbox.git
cd plankton-toolbox
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

To run the application.

cd plankton-toolbox
source venv/bin/activate
python3 plankton_toolbox_start.py

Note that you must have the two directories "plankton_toolbox_data" and "plankton_toolbox_counter" in the same directory as the "plankton-toolbox_start.py" python file. They can be downloaded from http://nordicmicroalgae.org/tools

For Mac users that are using the pre build Mac version these two directories should be placed in the users home directory.