Application id: researcher: Young / Independent

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APPLICATION ID:

RESEARCHER: Young / Independent


Curriculum Vitae





Personal information




First name / Family name

Nathalie Gorretta

Address(es)

763, chemin des charretiers 34270 st jean de cuculles

Telephone

+33467046311







Mobile

+33 677551038

E-mail

Nathalie.gorretta@irstea.fr

Nationality

French

Date of birth

16/02/1966

Gender

Female







Personal statement

Based on my background and skills in computer science and signal image processing my research focus is the development of innovative approaches to process high dimensional data, such as spectra and multispectral or hyperspectral images acquired on natural scenes or biological objects. I have published 27 papers in peer review journals, 14 conference papers and 3 book chapters. My published papers have been cited a total of 159 times (Scopus data base, October 2017).

I participated to several research projects funded by French national agencies (ANR) or European community.

I supervise thesis and master’s students (French pdh student but also foreign students) and also take part in the initial training by giving courses in image analysis and data processing.

This fellowship will be a crucial opportunity for me to achieve my career objectives. Specifically, my existing skills in multivariate data processing will greatly increase by becoming embedded in a world class research group led by Prof. Gowen but also facing new hyperspectral image modalities (e.g. fluorescence, temporal acquisitions) and new processing challenges (e.g. data fusion, time series modelling). My knowledge about pathogen development on biological samples will be also greatly strengthened and expanded with collaboration of UCD specialists in this domain (Crop Science unit, School of Agriculture & Food Science, UCD) facilitating for example future research on plant diseases detection in constraints environment (e.g. in fields). The skills and experiences gained during the fellowship will add to my professional portfolio. It will be placing me in a strong position to develop new research ideas, independent research funding, re-enforce my tenured position by accomplishing a professional thesis (HDR or “Habilitation à Diriger la recherche”) in data modelling and hyperspectral imaging. This will allow me to lead my own team of students and fellows.



Break career :

  • Phd was paused between May 2006 to September 2007 following maternity leave (birth of twins and serious health problem for one of them).

  • 20/11/1997 to 01/04/2000: Work stoppage due to a serious accident in public road traffic (hospitalization and rehabilitation).

Education and training

Please provide information regarding your Ph.D. and M.S

Location and dates

Montpellier, France – 01/09/2005-25/02/2009

Title of qualification awarded

PhD degree, Graduate school of computer sciences

Principal subjects/occupational skills covered

A segmentation approach for Hyperspectral imaging combining chemometrics and image processing tools.

Most of the methods developed for HSI processing perform data analysis without taking into account spatial information. Each pixel is considered individually, as a simple array of spectral measurements, with no specific arrangement. Considering the available spectral and spatial information is of major importance to enable processing of complex images. During this PHD, I developed a new generic method to combine spectral and spatial aspects in a symmetric and iterative way. This thesis produced 3 papers with a total of 20.

Skills covered: image analysis, chemometrics, data analysis.


Name of Institute

University of Sciences, Montpellier






Location and dates

University of sciences, Montpellier and Silsoe Research Institute (SRI), Silsoe, United Kindom. – 01/09/2002-30/06/2003

Title of qualification awarded

Master degree in computer sciences,

Principal subjects/occupational skills covered

Cabbage/weed discrimination with a region/contour based segmentation approach for multispectral images.

In this master thesis, I developed segmentation algorithms dedicated to complex and multi-spectral images and used a collaborative edge-segmentation strategy to discriminate cabbage and weeds in multispectral images from the field.



Name of Institute

University of sciences, Montpellier







Location and dates

Lyon – France 01/09/1992-30/06/1995

Title of qualification awarded

Bachelor of Engineering

Principal subjects/occupational skills covered

Signal and Image Analysis and processing

Name of Institute

National Institute fo applied sciences, electrical engineering department (INSA).

Work experience

Location and dates

Montpellier, France - 25/02/2009 to present

Occupation or position held

Researcher Irstea - Joint Research Unit ITAP, Montpellier, France. Team COMiC (Optical Sensors for Complex Material).

Main activities and responsibilities

I’m a member of the the ‘COMIC’ research team which designs optical sensor in accordance with agricultural and environmental specifications (i.e. low cost and robust).

My principal responsibilities concern:



  • Research student monitoring and supervision,

  • Development of multi-spectral and hyperspectral data processing tools

  • Equipment design to optimise spectra or image quality,

  • Management and Co-management of research projects (setting up scientific project, fund raising and financial setup, project management and communication) with partners.

Name of employer

Institut national de recherche en sciences et technologies pour l’environnement et l’agriculture (IRSTEA)



Location and dates

Montpellier, France - 2000-2005

Occupation or position held

Research engineer, Cemagref– Joint Research Unit ITAP, France. Team IODE (instrumentation, optics and decision).

Main activities and responsibilities

  • Development of image processing tools for multispectral images;

  • Design of image acquisition systems;

  • Implementation et monitoring of experiments;

  • Management of Regional projects (setting up scientific project, fund raising and financial setup, project management and communication):

  • Real time detection of pit in peaches line process using NIR imaging system. (regional grant “COST”) (Role: project leader).

  • Density measurement of must fermentation using pressure sensors (Role: co-leader project).

Name of employer

  • Centre d’étude du machinisme agricole et des eaux et forêts(Cemagref)



Location and dates

Montpellier France , 1995-1997

Occupation or position held

Research engineer Team Giqual (instrumental engineering for food quality)

Main activities and responsibilities

  • Development of image processing tools for B&W and color images;

  • Design of image acquisition systems;

  • Implementation and monitoring of experiments;

  • Involved in different research projects :

  • Real time assessment of the quality of the harvest using Black and white imaging systems (Project funding by NewHolland company).

  • Assessment of bunch quality (size of the berries, color) using color imaging system (Project funding by aregional company).

  • Orchard sprayers: an european program to compare testing methods.

Name of employer

Centre d’étude du machinisme agricole et des eaux et forêts(Cemagref)


Languages




Mother tongue(s)

French

Other language(s)




Understanding

Speaking

Writing

European level (*)




Listening

Reading

Spoken interaction

Spoken production




English




C1

C1

B2

B2

B2

Spanish




A2

B1

A2

A1

A1




(*) Common European Framework of Reference for Languages http://europass.cedefop.europa.eu/en/resources/european-language-levels-cefr

Academic Record

Add as many lines as needed, delete fields which are not relevant to your profile

Publications


Accepted, in press and published articles / papers:

Among my published articles, highlights relevant to this proposal include:



  • My first experience on the processing of hyperspectral imaging using discriminant analysis (Gorretta, 2006). This is my highest cited paper.

  • The development of a spectral-spatial approach to process hyperspectral imaging (Gorretta, 2012). This paper presents, in my opinion, an original and a generic way to combine both dimensions of hyperspectral images.

  • The detection of low concentration compounds in hyperspectral images (Boiret, 2016, and Mishra, 2015). This problem is an active field of research whatever the area of application (agriculture, pharmaceutical, food industry …). Those articles concerns my first steps in this difficult and important topic.

  • The development of a physical model for retrieving foliar biochemistry using close-range imaging spectroscopy (Jay, 20016). This paper presents, in my opinion, an original and an alternative way to address the detection of an-typical and weak signal in vegetation (e.g. disease detection).

  • Jay, S; Gorretta, N; Morel, J; Maupas, F; Bendoula, R, Rabatel, G; Dutartre, D; Comar, A; Baret, F; 2017. Estimating leaf chlorophyll content in sugar beet canopies using millimeter-to centimeter-scale reflectance imagery, Remote Sensing of Environment,198,,173-186,.,doi.org/10.1016/j.rse.2016.02.029. (I.F:7.388).

  • Nouri, M., Gomez, C., Gorretta, N., Roger, JM., 2017. Clay content mapping from airborne hyperspectral Vis-NIR data by transferring a laboratory regression model, Geoderma, 298, 54-66. doi.org/10.1016/j.geoderma. 2017.03.011. (I.F.=3.310).

  • Al Makdessi, N., Jean, P-A., Ecarnot, M., Gorretta, N., Rabatel, G., Roumet, P., 2017. How plant structure impacts the biochemical leaf traits assessment from in-field hyperspectral images: A simulation study based on light propagation modeling in 3D virtual wheat scenes, Field Crops Research, 205, 95-105. doi.org/10.1016/j.fcr. 2017.02.001. (I.F.=3.541).

  • Adeline, KRM., Gomez, C., Gorretta, N., Roger, J-M., 2017. Predictive ability of soil properties to spectral degradation from laboratory Vis-NIR spectroscopy data, Geoderma, Volume 288, 143-153. Predictive ability of soil properties to spectral degradation from laboratory Vis-NIR spectroscopy data. doi.org/10.1016/j.geoderma. 2016.11.010. (I.F.=3.310).

  • Jay, S; Bendoula, R., Hadoux, X., Féret, J-B., Gorretta, N., 2016. A physically-based model for retrieving foliar biochemistry and leaf orientation using close-range imaging spectroscopy, Remote Sensing of Environment, 177, 220-236. doi.org/10.1016/j.rse.2016.02.029. (I.F.:7.388).

  • Hadoux, X., Kumar, D-K., Sarossy, M-G., Roger, J-M., Gorretta, N. 2016. Application-Dedicated Selection of Filters (ADSF) using covariance maximization and orthogonal projection, Analytica chimica acta, Volume 921, Pages 1-12. doi.org/10.1016./2Fj.aca. 2016.04.004. (I.F.=4.712).

  • Boiret, M., Gorretta, N., Ginot, Y-M., Roger, J-M., 2016 An iterative approach for compound detection in an unknown pharmaceutical drug product: Application on Raman microscopy, Journal of pharmaceutical and biomedical analysis, 120, 342-351. doi:10.1016/j.jpba.2015.12.038. (I.F.=2.904).

  • Boiret, M., de Juan, A., Gorretta, N.; Ginot, Y-M., Roger, J-M., 2015. Setting local rank constraints by orthogonal projections for image resolution analysis: Application to the determination of a low dose pharmaceutical compound, Analytica chimica acta 892, 49-58, doi.org/10.1016/j.jpba.2013.11.025. (I.F.=4.712).

  • Mishra, P; Herrero-Langreo, A., Barreiro, P., Roger, J-M, Diezma, B., Gorretta, N., Lleó, L., 2015. Hyperspectral to multispectral imaging for detection of tree nuts and peanut traces in wheat flour, Journal of Spectral Imaging,4,1,1-9. doi.org/10.1255/jsi.2015.a2.

  • Hadoux, X, Jay, S. Rabatel, G., Gorretta, N., 2015. A spectral–spatial approach for hyperspectral image classification using spatial regularization on supervised score image, IEEE Journal of Scteeled Topics in Applied Earth Observations and Remote. Sensing, 8, 2361-2369.doi.org/10.1109/JSTARS.2014.2347414 (I.F.=2.145).

  • Mishra, P., Herrero-Langreo, A., Barreiro, P., Roger, J-M., Diezma, B., Gorretta, N., Lleó, L., 2015. Detection and quantification of peanut traces in wheat flour by near infrared hyperspectral imaging spectroscopy using principal-component analysis, Journal of Near Infrared Spectroscopy, 23(1), 15-22. doi.org/10.1255/jnirs.1141 (I.F.=1.480).

  • Jay, S., Rabatel, G., Hadoux, X., Nouri, M., Moura, D., Gorretta, N., 2015. In-field crop row phenotyping from 3D modeling performed using Structure from Motion, Computers and Electronics in Agricultre, 110,70-77. doi.org/10.1016/j.compag.2014.09.021 (I.F.=2.365).

  • Boiret, M., de Juan, A., Gorretta, N., Ginot, Y-M., Roger, J-M., 2015. Distribution of a low dose compound within pharmaceutical tablet by using multivariate curve resolution on Raman hyperspectral images, Journal of pharmaceutical and biomedical analysis, 103, 35-43. doi: 10.1016/j.jpba.2014.10.024 (I.F.=2.904).

  • Hadoux, X., Gorretta, N., Roger, J-M., Bendoula, R., Rabatel, G. 2014 Comparison of the efficacy of spectral pre-treatments for wheat and weed discrimination in outdoor conditions, Computers and Electronics in Agriculture,108,,242-249. doi.org/10.1016/j.compag.2014.08.010 (I.F.=2.365).

  • Boiret, M., Rutledge, D., Gorretta, N., Ginot, Y-M., Roger, J-M., 2014. Application of independent component analysis on Raman images of a pharmaceutical drug product: Pure spectra determination and spatial distribution of constituents, Journal of pharmaceutical and biomedical analysis, 90, 78-84, (IF=2.904).

  • Rabatel, G., Gorretta, N., Labbe, S. 2014. Getting simultaneous red and near-infrared band data from a single digital camera for plant monitoring applications: Theoretical and practical study, BiosystemsEngineering117,doi.org/10.1016/j.biosystemseng.2013.06.008 (I.F.=2.063).

  • Kobori, H, Gorretta, N.; Rabatel, G., Bellon-Maurel, V., Chaix, G., Roger, J-M., Tsuchikawa, S., 2013. Applicability of Vis-NIR hyperspectral imaging for monitoring woodmoisture content (MC), Holzforschung, 67(3), 307-314. doi.org/10.1515/hf-2012-0054 (I.F.=1.711).

  • Gorretta, N., Rabatel, G., Fiorio, C., Lelong, C., Roger, J-M., 2012. An iterative hyperspectral image segmentation method using a cross analysis of spectral and spatial information, Chemometrics and Intelligent Laboratory Systems, 117, 213-223. doi.org/10.1016/j.chemolab.2012.05.004 (I.F.=2.595).

  • Gorretta, N., Rabatel, G., Roger, J-M., Fiorio, C. Lelong, C., Bellon-Maurel, V., 2008. Hyperspectral imaging system calibration using image translations and Fourier transform, Journal of near infrared spectroscopy,16(4),371-380, doi.org/10.1255/jnirs.809 (I.F.=1.411).

  • Gorretta, N., Rabatel, G., Roger, J-M., Fiorio, C. Lelong, C., Bellon-Maurel, V.2006. Vitreousness of durum wheat kernels using near infrared hyperspectral imaging,.Journal of Near Infrared Spectroscopy,14(4,)231-236. doi.org/10.1255/jnirs.640 (I.F.=1.411).

Submitted publications:

  • Morel, J., Jay S., Bendoula, R., Ferret, J-B., Gorretta, N. Assessing the physiological impact of plant diseases on leaf tissues using the PROCOSINE radiative transfer model and close-range hyperspectral imaging: a case study with banana leaf pathogen M. fijiensis».Remote Sensing of Environment, Submitted in September 2017.

  • Nouri, M, Gorretta, N., Vaysse, P., Roger, J.M. « Series of NIR hyperspectral image of healthy and infected apple tree leaves for the early detection of apple scab disease».Data in Brief, Submitted in July 2017.

  • Gomez, C., Adeline, K., Bacha, S., Driessen, B., Gorretta, N., Lagacherie, P Roger, JM., Briottet, X. Evaluating the sensitivity of clay content prediction to spectral configuration of VNIR/SWIR imaging data, from multispectral to hyperspectral scenarios. Remote Sensing of Environment, Submitted June 2017.

  • Gorretta N. , Hue C., Roger J.M. , « Processing SDS-PAGE gels of proteins by means of image processing and chemometrics : application to evaluate the impact of fermentation on cocoa beans (Theobroma cacao L.) from various origins”. Talanta, submitted in october 2017.

Presentations as invited speaker




Authored books or book chapter(s)

  • Gorretta, N., Gomez, C. Chapter 18 - Spectral–Spatial Unmixing Approaches in Hyperspectral VNIR/SWIR Imaging. In: Cyril R, editor. Data Handling in Science and Technology: Elsevier; 2016. p. 579-611. doi.org/10.1016/B978-0-444-63638-6.00018-8.

  • Bellon-Maurel, V. and Gorretta, N., 2014. NIR Hyperspectral Imaging for Food and Agricultural Products, in Infrared and Raman Spectroscopic Imaging : Second, Completely Revised and Updated Edition (eds R. Salzer and H. W. Siesler), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527678136.ch7.

  • Cointault, F., Journaux, L., Rabatel, G., Germain, C., Ooms, D., Destain, M-F., Gorretta, N., Grenier, G., Lavialle, O., Marin, A., 2012. Texture, Color and Frequential Proxy-Detection Image Processing for Crop Characterization in a Context of Precision Agriculture, Agricultural Science, Dr. Godwin Aflakpui (Ed.), InTech, doi: 10.5772/36674.

Participation in open calls for proposals as contributor or leader

  • Participation to two ANR open calls (French research Agency) as co-leader and leader respectively (2014, 2015). In both cases, the project was not accepted.

  • Participation to Agropolis foundation calls (Montpellier, 2015). Proposition not accepted.

  • Participations to agropolis Fundation calls (French regional call).

  • Participation to Muse Call (University of Montpellier) as leader. Proposal in progress.

Graduate teaching as lecturer or training coordinator

  • Courses in master (Agrotic, 30 H/year) – Hyperspectral imaging and chemometrics.

  • Courses in imaging: 3rd year of engineering school Montpellier Sup Agro (8H) and Master I "Biology and health" UMII University of Montpellier (8H).

Awards and prizes, if any




Collaboration and Networking

Participation in collaborative projects funded by competitive programmes (specify if at leading position)




  • 2010-2014: RHEA, Robot fleets for Effective Agriculture, European Project (FP7-NMP-2009-LARGE-3). Total Funding: €6.9 M. Role: Involved in WP3 (Perception system).

RHEA was focused on the design, development, and testing of a new generation of automatic and robotic system for weed management. WP3 was dedicated to the design of the final vision system for weed/crop differentiation (required wavelength, resolutions, synchronised artificial lighting). My responsibilities in this project were (1) the supervision of a PhD student for the development of hyperspectral data processing tools to detect weed in crops (2) the design of the embedded imaging device.

2011-2020: Projet Aker (National French Research Agency ANR). Total Funding €420 k. Role: involve in WP3 (hyperspectral imaging).

Development of a rapid phenotyping system for beet using optical sensors Project in collaboration with many actors including the French Beet Institute (IFB).

2012-2015 : Project Phenome (National French Research Agency ANR). €100 k. Role: involve in WP2.

Development and valorisation of new-generation phenotyping tools for the analysis of genetic determinants of nitrogen fertilizer use efficiency in soft wheat.

  • 2017-2018: PHENOBET, CASDAR project (French Ministry of Agriculture funding).Total Funding €300 k. Role:

Data fusion of optical sensors and cultural models to characterize sugarbeet varieties (phenotyping). Besides project management, my responsibilities include supervision of two post-doc researchers for the development of hyperspectral or multispectral imaging tools to estimate chemical and structural variables (e.g. Leaf area index, chlorophyll content).

  • 2015-2018: AVENTURIA: CASDAR project (French Ministry of Agriculture funding). Total Funding €300 k. Role: Project co-Leader.

Early detection of fungal diseases on apple trees by hyperspectral imaging. My responsibilities in this project concern the supervision of a PhD student and a post-doc researcher, the development of physical models for early detection of fungal diseases.

  • 2017-2021: OPTIPAG: Optics for Precision Agriculture. (ANR générique 2016, défi 1: Gestion sobre des ressources et adaptation au changement climatique), Total funding 486 k. Role: Involved in WP2 and WP3 (Optical and Processing packages). This project will gather modern optical techniques to probe vegtables in a non-invasive way and promote a better understanding of internal and external transfer processes, including retroaction on the production, optimization, stress (dryness) and diagnostic. My responsibilities in the project include (1) equipment design (2) data processing using various chemometric approaches to select the most appropriate acquisition techniques or to combine them.

Partnerships or experience with industry

Over the course of my career, I have been able to carry out numerous collaborative projects with industry on a variety of projects: New-holland Braud (detection of the quality of raisains by imaging on harvesting machine) , Arterris detection of wheat quality by hyperspectral imaging, Arvallis detection of wheat quality by hyperspectral imaging, Pellenc-ST (Implementation of chemometric approaches for waste sorting) …

University or post-graduate programme leader




Graduate teaching as lecturer or training coordinator; PhD supervision



Membership of professional bodies and committees

  • Secretary to the Association Heliospir (to promote the use of Near Infrared spectroscopy).

  • National Staff representative for promotion (joint administrative commission or CAP).

  • Member of scientific council of the research unit ITAP (Irstea, Sup-Agro joint unit).


Research management, Technology transfer, and Communication

Team management




Technological platform management

Hyperspectral imaging plateform management.

Consultancy for the public or private sector










Other experience and skills relevant to the application




Scientific References Add up to 3 references

Full name

Bellon-maurel Véronique

Position

Head of department echotechnologies

Institution

Irstea

Email address

Veronique.bellon@irstea.fr



Full name

Roger Jean-Michel

Position

Research director

Institution

Irstea

Email address

Jean-michel.roger@irstea.fr



Full name

Fiorio Christophe

Position

Computer science Professor

Institution

University of Montpellier Laboratory of informatics, Robotics and MicroElectronics, Montpellier France

Email address

Christophe.fiorio@lirmm.fr



Full name

Anna de Juan Capdevila

Position

science Professor

Institution

University of Barcelona, Solution equilibria and chemometrics group

Email address

Anna.dejuan@ub.edu

How did you hear about AgreenSkills programmes?

Please indicate here how you first heard of the AgreenSkills+ programme (e.g. university call for applications, job mailing list/website, magazine advertisement, network, etc.)

Informed of my wish to stay abroad, it was the international management of my institute that told me about the Agreenskill call.



CV AgSk+ August 2016 First name / Family name – Date


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