The Plankton Toolbox is a free tool for aquatic scientists, and others, working with environmental monitoring related to phyto- and zooplankton.
- 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 is available here:
The latest version of Plankton Toolbox is available for MacOS and Windows at: http://nordicmicroalgae.org/tools
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.
If there are problems, of any reason, to run the Windows executable file, then it is always possible to run Plankton Toolbox as a Python application. Here is an example of how to do it on Windows.
Download and install Python ( https://www.python.org/downloads/ ). In the example below Python version 13.3 was installed here: "C:\Python313".
Create a folder named "PTBX" on the desktop and move into it.
cd Desktop
mkdir PTBX
cd PTBX
Download and install the software for Plankton Toolbox from GitHub.
git clone https://github.com/planktontoolbox/plankton-toolbox.git
cd plankton-toolbox
C:\Python313\python.exe -m venv venv
venv\Scripts\activate
pip install -r requirements.txt
Create a file in the PTBX folder with the name "Start_PTBX.bat". Add the line below to that file.
plankton-toolbox\venv\Scripts\python.exe plankton-toolbox\plankton_toolbox_start.py
Now Plankton Toolbox can be started by a double klick on that bat file, but there is still one important step left.
To get species lists and settings for microscopes, etc., you have to replace the two folders called "plankton_toolbox_data" and "plankton_toolbox_counter" with the ones that are published here http://nordicmicroalgae.org/tools as parts of the zip files. Both "plankton_toolbox_data" and "plankton_toolbox_counter" should be placed in the folder called "PTBX" if the example above is followed.