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Software dedicated to data storage and counting of phytoplankton as well as the calculation of the IPLAC index (WFD requirements).

The Phytobs software has been developed since 2009 to meet the need for a phytoplankton counting tool independent of commercial and cross-platform software (Windows, Linux and Mac OS) allowing the data storage. It is built around a database in MySQL and runs through an application developed in JAVA.

Since some versions, Phytobs can be run locally (on a PC) or networked on a server (for multi-user use) and its interface can be displayed in French, English, Polish or Spanish (soon in other langages).

thus, the application constructed includes 4 modules:
– management of taxa and calculations of unitary biovolumes,
– counting under the microscope,
– IPLAC index calculation,
- IPHYGE index calculation.

The Phytobs counting module allows the assisted input (by code use) of sample taxa records and  counting with 2 counting strategies per sample. Counts (number of cells or individuals per ml) and corresponding biovolumes (mm3/l) are automatically calculated and stored. Since version 3.2, the results are also presented in the form of a synthesis by algal groups (abundance, biovolume, relative biovolume and carbon contents) and specify the biovolume of potentially toxic cyanobacteria with the indication of the corresponding potential toxins (in accordance with the list defined in the ANSES collective expertise work).

The phytoplankton taxa management module includes taxonomically up-to-date denominations with the most common synonyms of all the algal groups encountered in phytoplankton samples (over 10000 denominations to date). Individual biovolumes can be calculated on existing taxa or new ones added by the user.

The IPLAC module of Phytobs allows the calculation of the Phytoplankton Lacustrine Index (Laplace-Treyture & Feret, 2016) [1] implemented for the assessment of the ecological status of water bodies in France.

The IPHYGE module of Phytobs allows the calculation of the Phytoplankton Index in large rivers (Meyer et al., 2023) [2] implemented for the assessment of the ecological status of large rivers in France.

Finally, all the data produced and stored can be exported in csv format: database type, free or according to the recommendations for the exchange of national data. The outputs of the IPLAC and the IPHYGE calculations also provide a summary pdf of the index calculation per water body and river.

Phytobs is interactive and open: released free under GNU GPL license, the code is accessible to developers who wish, to ensure the evolution, improvement and adaptation of this tool to a panel of uses and users as wide as possible.

[1] C. Laplace-Treyture, Thibaut Feret, 2016. Performance of the Phytoplankton Index for Lakes (IPLAC): A multimetric phytoplankton index to assess the ecological status of water bodies in France. Ecological Indicators. Vol 69, October 2016, Pages 686-698

[2] Meyer, A., Prygiel, E., Laplace-Treyture, C., 2023. DIPCEAU : Développement d’un Indicateur Phytoplancton pour l’évaluation de l’état écologique des Grands Cours d’Eau. Action 3 : mise au point de l’indicateur IPHYGE. Création et sélection de métriques (Rapport final). INRAE Nouvelle Aquitaine Cestas, Gazinet, FRA.

File download

PHYTOBS v3.2.4 Full installation

Download	1- MySQL MySQL software (essential to Phytobs). Download from the MySQL site the mysql-installer-community-8.0.xx.0.msi file (the one below)	html link	09/04/24	New version of the phytoplankton counting software: counting, biovolume calculation, data export and index calculations (IPLAC, IPHYGE). More than 10300 taxa names with synonymy and potential cyanotoxins are provided
Download	2- PHYTOBS Software for counting, banking phytoplankton samples and calculating IPLAC and IPHYGE indices (executable)	.exe (181 Mo)	v3.2.4 09/04/24
Download	3- Instructions Installation instructions	.pdf (1.1 Mo)	06/07/22

PHYTOBS v3.2.4 Update  

Download	1- PHYTOBS Update of the counting software from a version 3.x	.exe (25.6 Mo)	v3.2.4 09/04/24	Update of  the phytoplankton counting software including the IPHYGE index calculation, new taxa names, translation in Polish and a alert of the availability of a new version on the website
Download	2- Instructions Update instructions	.pdf (208.8 Ko)	06/07/22

Download

PHYTOBS patch v3.1.1 to v3.1.2 Fix for the counting software from version 3.1.1 to version 3.1.2

.exe (9.3 Mo)

v3.1.2 11/03/19

March 2019 patch allowing the switch from version 3.1.1 to version 3.1.2 (correction of Import/Export function)