Presentation

Plankton Identifier is a free software which allows the automatic identification of objects (plankton and/or particles) from a set of images with their associated data. Therefore, before you can use Plankton Identifier, you must extract object data (PID format) and object thumbnails (JPEG format) with a dedicated hardware-software combination such as ZooScan and ZooProcess (http://www.ZooScan.com).

Once data acquisition is done, Plankton Identifier helps the user to build a Learning File (set of objects identified by an expert) through a safe interface which prevents from data loss, erroneous duplicates etc. Then, using the learning file, Plankton Identifier allows the automatic recognition of an unlimited number of objects from one or several data files. Additionally, the user can optimize the recognition by many ways (by choice of different data analysis methods, selection of variables, variable transformation, way of grouping objects etc.). Results are stored in one or several text files which can easily be imported in other softwares (for graphics, time series analysis etc...). A detailed statistical report is also generated (html format allowing copy-paste).

NOTE: Although Plankton Identifier has been initially developed to identify Planktonic organisms, it can virtually identify any kind of objects.

Supervised learning algorithms are not implemented in Plankton Identifier itself but are those of the free data mining software TANAGRA which is used in batch mode. This is the reason why you must install Tanagra 1.4.22 or above on your computer before using Plankton Identifier.

TANAGRA can be downloaded here.

NOTE: Experimented users can define their own data analysis methods for Plankton Identifier using Tanagra tdm format.

 

Downloads

Version currently available is 1.2.6. It is a Win32 application running under Windows XP, Windows 2000 and Windows 98. A screen resolution of at least 1024x768 (96 ppp only) is highly recommended. There is no UNIX, LINUX or MacOS version.

To install Plankton Identifier click on the link below and save the installer on your computer. Then, execute the installer and follow the instructions.

Seven recognition methods (all tested) are currently installed with Plankton Identifier as well as several methods to test classifier performances. Some demo files (zooplankton JPEG images and PID files) are included and will be installed in a 'Demo' subfolder.

DOWNLOAD PLANKTON IDENTIFIER (31 Mo)

An additional application, PID Viewer, can be downloaded separately. PID viewer helps to visualize PID files information (header, data, and basic statistics). Once PID viewer is installed on your computer, you just have to double-click on PID files (Sample or Learning) to easily explore and/or compare their contents, even from Plankton Identifier.

DOWNLOAD PID VIEWER (0.5 Mo)

NOTE: PID Viewer is not an editor. Manual edition of a PID file is not recommended but if necessary you can use any usual text editor.

Please, don't forget to mention Plankton Identifier when you produce results, notably in scientific publications. You can refer to Plankton Identifier as follow:

Gasparini Stéphane (2007). PLANKTON IDENTIFIER: a software for automatic recognition of planktonic organisms. http://www.obs-vlfr.fr/~gaspari/Plankton_Identifier/index.php

 

Support

More information about the use of Plankton Identifier is available in the User Guide.

If you experience problems during installation, if you don't know how to make choices among options or if you don't know how to interpret the results, you can also look at the F.A.Q.

You can also post your questions or exchange information about Plankton Identifier on the Zooscan forum.

 

Known limitations

- Each PID file (sample) can contain an unlimited number of objects but it is not possible to analyse more than 392 PID files at once.

- All files (Sample and/or Learning) used in one analysis must have exactly the same variables (same order, same names). If you have files with different variables, use them in separate analysis.

- Analysis conducted with corrupted PID files can produce unexpected results. If you modify PID files manually, be sure you know what you are doing ! Look at the User guide for more information about PID files expected format.

 

Version history

 

Sources

Plankton Identifier has been developed using Delphi 2005 PE (Codegear from Borland), which is free under conditions, and the free components Virtual Treeview (Soft-Gems) and VirtualShellTools (Mustangpeak). PID viewer uses the free Delphi component Toneinstance (bome.com). The installers have been created using Inno setup 5.1.9 (Jordan Russell's software). Plankton Identifier and PID viewer source codes are available on demand for non commercial purpose.

 

Acknowledgements

Thanks are due to Elvire Antajan, Ricco Rakotomalala, Marc Picheral and Gaby Gorsky for support and contribution to this project.

 

Some additional links

ImageJ : Free image analysis software (+ source code in Java)
ImageTools : Free image analysis sofware for Windows ( + source code in C)
NIH-image: Free image analysis software for MacOS (+source code in Pascal)
efg's computer lab: Technical informations about image processing, algorithms and much more.

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Stéphane Gasparini
Laboratoire d'Océanographie de Villefranche
UMR 7093 - CNRS / Université Pierre et Marie Curie - Paris 6
BP 28 - 06234 Villefranche sur mer Cedex - France

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Last Update : 02-Sep-2009