Partners & Workplan
- the production of a system of image analysis that significantly upgrades the existing systems in terms of the accuracy of cellular bio-volume quantification; such an upgrade will be developed;
- methodological standardization and certification of ecological descriptors of the state of health of aquatic ecosystems based on the analysis of the dimensional structure of the phytoplankton communities;
- the production of data analysis software, linked to image analysis software, that produces a classification of the ecological status of the ecosystems from which the samples were taken, in accordance with the methodology set out in current Italian laws (Legislative Decree 152/99 and subsequent modifications) and the EU-WFD (60/2000/EC), in the process of being implemented on the national level;
- the transfer of the results acquired to interested parties by means of the implementation of a training course specializing in two fields.
Project Activities – For the fulfillment of the objectives, there will be a series of project activities organized into 5 Workpackages (WPs).
Workpackage 1 (WP1): creation of 2D image analysis software for the determination of the bio-volumes and the cellular surfaces of algal genera in transitional and marine coastal environments
Workpackage 2 (WP2): Studies in the field and innovative strategies for the monitoring and conservation of transitional and marine-coastal environments
Workpackage 3 (WP3): Creation of the software for the determination of the non-taxonomic descriptors and for the evaluation of the state of health of aquatic ecosystems
Workpackage 4 (WP4): Training Course entitled “Methodological issues related to the use of morphometric descriptors of phytoplankton corporations in the evaluation of the state of health of transitional and marine-coastal ecosystems.
Workpackage 5 (WP5): Management of the project
The specific objective of WP1 is the creation of one software packages for the analysis of images, optimised for the two dimensional representations obtainable with various models of Nikon Instruments inverted microscopes, equipped with USB or firewire cameras that enable the evaluation of one-dimensional morphometric characteristics (length, width, thickness, perimeter); two-dimensional morphometric characteristics (cellular surface) and three-dimensional morphometric characteristics (cellular bio-volume) of the algal cells, in routine analysis, using instrumentation commonly available in the Laboratory. The software will be designed in such a way as to have the broadest distribution possible on the national and international level and will be designed to work with Nikon microscopes. WP1 includes the development of the following activities (T1-T10), which will be carried out by Research Units 1 and 2 (RU1 and RU2) in collaboration with the private companies that are participating in the project.
The objective of WP2 is to proceed with the methodological standardization and certification of the ecological descriptors of the state of health of aquatic ecosystems based on the analysis of the dimensional structure of the phytoplankton communities. The activity for each task is specified:
- the southern Pacific (i.e. Polynesia and New Caledonia),
- marine-coastal transitional environments along the coasts of Brazil,
- transitional environments typical of the North Sea and Atlantic eco-region, as well as, for comparison,
- ecosystems with different levels of human impact in Puglia, including both transitional ecosystems and marine-coastal ecosystems.
- the dimension of the sample (n° of cells to be counted and measured) necessary for the accurate analytical determination of the values of the characteristic (coefficient of variation of the average ≤ 10%);
- the relations existing between the dimension of the sample and density of the phytoplankton corporations;
- the number and optimal position of the sampling stations for each ecosystem as a function of [3a] the surface area of the ecosystem, [3b] water circulation; [3c] the types of habitat in the sediments.
- The suitability of the diverse characteristics for describing perturbation pressure;
- The accuracy of the size-abundance distribution descriptors as descriptors of the ecological status of transitional ecosystems;
- The optimal model of classification for each of the descriptors selected (linear vs. type 3 functional response)
- The distribution of the normalized values into classes of ecological status, in accordance with the different national and international regulations in force (in Europe in accordance with the Water Framework Directive)
The main objective of WP3 is the creation of a software programme for the quantification of the main taxonomic and non-taxonomic descriptors of the phytoplankton the classification of the state of health of the transitional and marine-coastal ecosystems. The software for the analysis of data and classification of the ecological status is conceived as an autonomous expansion of the image analysis system produced by WP1: an expansion, in that it will receive as input files the output files of the image analysis system, and autonomous in that the software for the analysis of data and classification will be broadly general in character and will also be usable with data relating to other biological ecosystem components such as zooplankton, macro-zoobenthos and ichthyic fauna, thus representing a highly qualified instrument for the classification of the ecological status of all aquatic ecosystems. The market for the software product may thus be generalized to all organisations that operate programmes for monitoring the state of health of aquatic ecosystems in Europe and North America, with possible expansion in the other ecological macro-regions.
The Workpackage entails the following tasks:
The Workpackage entails the following tasks:
The project includes the activation of a training plan relevant to the scientific issues tackled in the project.
For this project the following training plan is proposed:
Title of the training plan: Methodological Aspects linked to the use of morphometric descriptors of phytoplankton corporations in the evaluation of the state of health of transitional and marine-coastal ecosystems.
Location of the training plan: Laboratory of Ecology, Department of Biological and Environmental Science and Technology, Centro Ecotekne, 73100 LECCE (Italy)
Duration of the training plan: 2 weeks + 1 week
Proposed Start Date: 7th month (2-week module) 33rd month (1-week module)
Description of the training plan: The training plan has the aim of training and increasing the knowledge of personnel who are already qualified for the identification and the classification of phytoplankton species and the use of programming tools. Specifically, the course will follow three parallel training programs.
The first is the “ecological” training program, intended for students with skills in the field of phytoplankton biology; it will be designed to improve knowledge of the descriptors of the ecological status of aquatic ecosystems, in order to apply the technological product to monitoring programmes;
The second is the “ICT” training program, intended for students with computer skills in the sectors of image analysis and parallel and distributed programming; it will aim at enhancing skills in the use of tools for analysing biometric data and the dimensional structures of phytoplankton; specifically it will look at themes relating to image analysis, tools for evolutionary computation (Genetic Algorithms and Neural Networks), Parallel Computing and Grid Computing, Data Mining and the application of these concepts to the analysis of the state of health of the ecosystems.
The third is the “PMI and software for the environment” training program, intended for potential stakeholders such as representative of national and international environmental protection agencies and administrations involved in the monitoring plans for the protection of transitional and coastal marine ecosystems. They could be the potential users for acquisition of software. The training program will aim to presentation of software for the environment and at their use in the monitoring plans.
The training plan related to the ecological and ICT training programs will be organised into 10 training modules, which will be taught in the course of the first two weeks of the training plan. Some of the modules are common to both programs, others are specific, plus one training module (PMI and Software for the Environment) which will be developed in the 33rd month of the project which will entail practical activities aimed at the application and the validation of ICT tools for the evaluation of the state of quality of the aquatic ecosystems.
The implementation of the training plan involves both theoretical lessons in the classroom and practical activities in biology or computing labs, for which there will also be e-learning activities. The common training, for the first two training programs plans, will be designed: • to develop issues related to ecological principles of monitoring the state of quality of aquatic transitional and marine coastal ecosystems and in particular the use of phytoplankton as an indicator of the ecological status of these environments; • to develop aspects related to the new methodological approaches to classifying the state of health of aquatic environments based on non-taxonomic descriptors (i.e. size-abundance distributions) of phytoplankton corporations. The “ecological” training program will have the following objectives:
- to provide theoretical aspects that take account the most recent literature concerning morphology, taxonomy, classification and phylogenesis of phytoplankton corporations,
- to teach theoretical and methodological aspects of phytoplankton as bio-indicators of the ecological quality of the aquatic transitional and marine-coastal ecosystems
- to provide indications regarding the new methodological approaches to classifying the state of quality of the aquatic transitional and marine-coastal ecosystems based on the use of non-taxonomic descriptors, measured with optical microscopy techniques supported by image analysis systems.
- to teach, by means of practical activities, methods and criteria for the correct identification of species
- to teach, by means of practical activities, ways of recording phytoplankton descriptors, with particular reference to non-taxonomic descriptors, linked to the dimensional characteristics of the individuals, measured with optical microscopy techniques, and to train students in the use of specific software
- to provide indications for the evaluation of the criteria for the classification of the state of health by means of non-taxonomic descriptors and to train students in the use of specific software.
This objective will be fulfilled in the last week of the training plan
The “ICT” training program will have the following objectives:
- to provide general principles concerning image analysis systems
- to teach the general principles of evolutionary computation (genetic algorithms and neural networks)
- to teach the general principles of parallel and distributed programming and grid computing
- to teach the general principles of treatment of data and data mining in particular
Persons eligible for the training plan:
The course will be open to about 20 people resident in the EU.
The criteria for the selection of the participants are as follows:
- the student must hold a degree in Biological or Environmental Science or in Information and Communication Technology.
- almost the 50% of the student must be compatible with the figure of young researcher, i.e. he/she must be less than 35 years of age and have at least 4 years of experience in the specific sector of reference.
- the student must have previous experience in the field of the taxonomy of phytoplankton or in the field of software programming for image analysis systems.
- the student must be involved, in his/her institution of origin, in research specific to the sector.
The management of the project is designed to guarantee: (1) the coordination of the project activities, in terms of both scientific and administrative coordination, (2) the monitoring of the activities and the verification of the fulfilment of the objectives on time, (3) the correct functioning of the project in terms of execution of the tasks, coordination between partners and information flow, (4) the publication of the results, promotion of the products and planning of the project follow-up, and (5) the coordination of the relations between project group, institutions and interested parties.The project management activities are described in detail in the relevant section (2.6) of this project presentation module.
The professional figures involved: local personnel of RU1 and external consultant – Duration of activity: 36 month Start: 1 month