Plankton Toolbox – a new tool for working with plankton data

Large data sets on plankton biodiversity and abundance provide many opportunities for research and environmental monitoring, but may be time consuming to work with. As a part of the Swedish LifeWatch project SMHI has developed Plankton Toolbox, an open source stand-alone application which will make the process easier.

Modern database systems make it possible to access large data sets on plankton biodiversity and abundance, including the occurrence of harmful algal bloom species. This gives insights into geographical distribution of species, bloom development etc. Plankton Toolbox is a free software developed to aid researchers and conservationists working with and analysing plankton data.

Plankton Toolbox is mainly aimed at working with data from water samples analysed microscopically, but the software is applicable also to other data. The workflow includes importing data, a quality control step, ways to filter out data for specific purposes, functions for aggregating data, plotting tools and some tools for statistical analyses. Importing and exporting of data in different formats is supported. Data can also be exported to other software for advanced statistical analyses.

Swedish marine monitoring data, including phyto- and zooplankton data, is available at the National Oceanographic Data Centre at SMHI. Plankton Toolbox can import data downloaded from the database.

A first version of the software, Plankton Toolbox 1.0 was released in May 2014. The software has been developed using Python and runs on personal computers with Windows or MacOS. A Linux version is in development.

Plankton Toolbox is available for download at

A two day workshop for Plankton Toolbox users was arranged in May 2014. A second workshop is planned to be arranged in autumn 2015.