Dr Jonathan Weber, PhD in Computer Science

Associate Professor @ Université de Haute-Alsace

Lecturer @ ENSISA

Researcher @ IRIMAS

  • Image and video segmentation
  • Mathematical morphology
  • Template matching
  • Data Mining
  • Deep Learning

Latest news
July 2018 : Paper accepted at MICCAI 2018 !
February 6th 2018 : Start of Menuakent Birara PhD thesis
November 1st 2017 : Start of Mounir Bendali PhD thesis
October 15th 2017 : Start of Hassan Ismail Fawaz PhD thesis
August 1st-2nd 2017 : SYSIMIT meeting at definiens, Munchen
September 1st 2016 : Start of Bastien Latard PhD thesis
September 1st 2016 : New position at Université de Haute-Alsace

Since 2016 Associate Professor Université de Haute-Alsace
2012-2016 Associate Professor Université de Lorraine
2011-2012 Teaching and Research Assistant Université de Lorraine
2010-2011 Teaching and Research Assistant Université de Strasbourg
2007-2010 R&D Engineer Ready Business System
Since 2018 Co-Head of Master Computer Science and Mobility Faculty of Science and Technology, Mulhouse
Since 2017 Co-Head of Master UHA 4.0 UHA 4.0
2013-2016 Head of Multimedia and Web Department Saint-Dié Institute of Technology
2011 PhD in Computer Science Université de Strasbourg
2007 MSc in Computer Science Université de Strasbourg
Research Topics
Template-matching/Pattern recognition

My research work on template-matching is mainly focused symbol spotting in technical documents. In such document, the spotting is hard because it suffered from the overlapping of symbols. So, the template-matching operator has to be robust to information overlap which eliminate most of the classical operators. To overcome this issue, we design a new hit-or-miss transform operator able to deal with information overlap. I also develop softwares to illustrate the efficiency of our proposed approach. Currently, I am working on the fully automatization of the method through machine learning approaches and its application to new data types such as bill tickets. I have also worked on template-matching applied to remote sensing images.
In the context of the CHIST-ERA AMIS project I will work on overlaid text localization in news video.

Image and Video segmentation and simplification

Segmentation is often the first step of image understanding process. Our contributions in this domain are various but all based on interactive quasi-flat zones segmentation method. Initially designed for video segmentation, we work on the application of this method to different image types and problems such as image filtering, satellite images time-series classification and tree leaves segmentation.
I also participate in the supervision of the PhD thesis of Rachida Es-Salhi on the visual data database co-segmentation which is typically a research subject dealing with all the problems induced by the data deluge.

Mathematical Morphology in Color Image

As mathematical morphology needs ordering, its application to color image is not straightforward. In fact, there is no generic optimal vectorial ordering able to deal with every image processing problems in all color spaces. In this context, we study existing vectorial ordering, design new ones and compare them through different image types and applications. We also work on the adaptation of existing morphologic tools to color image.

Research Projects
Name Type Date Involvment
TIMES ANR 2017-2020 Member
OPMoPS ANR/BMBF 2017-2020 Member
PLASIDIA AMI 2017-2018 Member
APIM PIR UHA 2017 Project Leader
Sys-MIFTA ERACoSysMed 2016-2019 Member
AMIS CHIST-ERA 2016-2019 Member
SYSIMIT BMBF 2015-2018 Member
ECOSGIL ANR-JC 2005-2008 Master Student
FoDoMuSt ACI 2004-2007 Master Student
(Co-)Supervised students
PhD student Date Subject
Mekuanent Birara 2018 - ... Mining videos and multimedia data
Mounir Bendali 2017 - ... Crowd behaviour analysis
Hassan Ismail Fawaz 2017 - ... Mining medical data
Bastien Latard 2016 - ... Semantic Analys of scientific articles
Master Student Date Subject
Hugo Besadoux 2018 Deep Learning applied to LIDAR data
Nirma Naruka 2018 Diaphragm segmentation in 3D imagery
Oleg Eremin 2017 Deep Learning applied to medical imagery
Rahul Sahal 2017 Overlaid text extraction in news video
Giovanni de Angelis 2016 People counting using 3D camera
Antonio Terrone 2016 People counting using depth image
Roberto Pisapia 2016 People counting using embedded systems
Julien Bidolet 2014 Graph indexing for image classification
Michał Kowalczyk 2012 Image segmentation on mobile environment
Jean-François Kraemer 2010 Video segmentation/annotation tool
Vincent Danner 2009 Optimized video management for Pelican


Pelican LogoPolyvalent Extensible Library for Image Computing and ANalysis is a multi-platform framework, written in Java, dedicated to Image Processing. The project started at the Université de Strasbourg in 2005 but its contributors are no longer in this university. It allows the processing of image from different types (2D, video, 3D, 3D+t) and origins (casual, medical, astronomic, remote sensing, ...) and contains many standard image processing algorithms.
Pelican contains more than 100k lines of code and is freely available under CC BY-NC 4.0 license.


CoastlineSoftware developped during the ANR-JC ECOSGIL project. Written in Java, it is a tool dedicated to geographers. It achieves several processing on coastal remote sensing images such as the extraction of coastline. It uses the Pelican framework. It is still used by geographers (initial release dated from 2007).


Symbol spotting exampleTeSySp (Technical Symbol Spotter) was initially developed to demonstrate our work on symbol spotting in technical documents. Written in Java, it is based on Pelican framework. It is an improvment of our initial approach, in particular the use of machine learning techniques to filter false-positives result. Moreover, TeSySp will allow to create ground-truth for symbol spotting and will contain different metrics to evaluate the quality of spotting results.

Institutions and departments
Since 2017 Information and Communication Department Faculty of Economics, Socials and Law studies, Mulhouse
Since 2017 Computer Science for Business Department Faculty of Science and Technology, Mulhouse
Since 2016 Computer Science Department École Nationale Supérieure d'Ingénieurs Sud-Alsace
2011-2016 Multimedia and Web Department Saint-Dié Institute of Technology
2013-2016 Computer Science Department Ecole Nationale Supérieure des Mines de Nancy
2009-2011 Computer Science Department Robert Schuman Institute of Technology
2009 Physical Measurements Department Louis Paster Institute of Technology
  • Web (HTML, CSS, PHP, Javascript, ...)
  • Operating Systems
  • Programming (C, C#, Java, Python, ...)
  • Database (SQL, UML)
  • Logic
  • Semantic Web
  • Artificial Intelligence
  • Content Management System
  • Mobile programming (Android)
  • Video game programming (Unity)
  • Project Management
  • Collaborative Tools
  • Security
  • Computer Graphics
  • Image processing
  • Mathematical Morphology
  • Data compression
  • Networks
jonathan [dot] weber [at] uha [dot] fr
+33 03 89 33 69 76
12, rue des frères Lumière
68093 Mulhouse FRANCE
Research Articles in International Journals
  1. Manuel Grand-Brochier, Antoine Vacavant, Camille Kurtz, Jonathan Weber, Laure Tougne,
    Tree Leaves Extraction in Natural Images: Comparative Study of Preprocessing Tools and Segmentation Methods,
    IEEE Transactions on Image Processing, Vol. 24, No. 5, pp. 1549-1560 (12 pages), May 2015
  2. François Petitjean, Jonathan Weber,
    Efficient Satellite Image Time Series Analysis Under Time Warping,
    IEEE Geoscience Remote Sensing Letters, Vol. 11, No. 6, pp. 1143-1147 (5 pages), June 2014.
  3. Jonathan Weber, Sébastien Lefèvre,
    Fast Quasi-Flat Zones Filtering Using Area Threshold and Region Merging,
    Journal of Visual Communication and Image Representation, Vol. 24, No. 3, pp. 397-409 (13 pages), April 2013.
  4. Jonathan Weber, Sébastien Lefèvre,
    Spatial and Spectral Morphological Template Matching,
    Image and Vision Computing, Vol. 30, No. 12, pp. 934-945 (12 pages), December 2012.
Communications to International Conferences and Workshops
  1. Hassan Ismail Fawaz, Germain Forestier, Jonathan Weber, Lhassane Idoumghar and Pierre-Alain Muller,
    Evaluating surgical skills from kinematic data using convolutional neural networks,
    Medical Image Computing and Computer Assisted Intervention (MICCAI), (8 pages), Granada, Spain, September 2018
  2. Bastien Latard, Jonathan Weber, Germain Forestier and Michel Hassenforder,
    Using Semantic Relations between Keywords to Categorize Articles from Scientific Literature,
    International Conference on Tools with Artificial Intelligence (ICTAI), (5 pages), Boston, USA, November 2017
  3. Bastien Latard, Jonathan Weber, Germain Forestier and Michel Hassenforder,
    Towards a Semantic Search Engine for Scientific Articles,
    International Conference on Theory and Practice of Digital Libraries (TPDL), (4 pages), Thessaloniki, Greece, September 2017
  4. Rachida Es-Salhi, Imane Daoudi, Jonathan Weber, Hamid El Ouardi, Saida Tallal, Hicham Medromi,
    Multi-scale image co-segmentation,
    Advances in Ubiquitous Networking: Proceedings of the UNet'15, Springer Singapore, pp. 381-390 (10 pages), Casablanca, Morocco, September 2015
  5. Erhan Aptoula, Jonathan Weber, Sébastien Lefèvre,
    Vectorial Quasi-flat Zones for Color Image Simplification,
    International Symposium on Mathematical Morphology (ISMM), Springer-Verlag Lecture Notes in Computer Science, Vol. 7883, pp. 231-242 (12 pages), Uppsala, Sweden, May 2013.
  6. Jonathan Weber, Salvatore Tabbone,
    Symbol spotting for technical documents : An efficient template-Matching approach,
    International Conference on Pattern Recognition (ICPR), 4 pages, Tsukuba, Japan, November 2012.
  7. Michal Kowalczyk, Bertrand Kerautret, Benoît Naegel, Jonathan Weber,
    Revisiting Component Tree Based Segmentation Using Meaningful Photometric Informations,
    International Conference on Computer Vision and Graphics (ICCVG), Springer-Verlag Lecture Notes in Computer Science, Vol. 7594, pp. 475-482 (8 pages), Warsaw, Poland, September 2012.
  8. Jonathan Weber, François Petitjean, Pierre Gançarski,
    Towards efficient satellite time series analysis: combination of Dynamic Time Warping and Quasi-Flat Zones,
    IEEE International Geoscience and Remote Sensing Symposium (IGARSS), pp. 4387-4390 (4 pages), Munchen, Germany, July 2012.
  9. Jonathan Weber, Sébastien Lefèvre, Pierre Gançarski,
    Interactive Video Segmentation based on Quasi-Flat Zones,
    International Symposium on Image and Signal Processing and Analysis (ISPA), pp. 265-270 (6 pages), Dubrovnik, Croatia, September 2011.
  10. Jonathan Weber, Sébastien Lefèvre, Pierre Gançarski,
    Spatio-temporal quasi-flat zones for morphological video segmentation,
    International Symposium on Mathematical Morphology (ISMM), Springer-Verlag Lecture Notes in Computer Science, Vol. 6671, pp. 178-189 (12 pages), Intra, Italy, July 2011.
  11. Jonathan Weber, Sébastien Lefèvre, Pierre Gançarski,
    Video Object Mining : Issues and Perspectives,
    IEEE International Conference on Semantic Computing (ICSC), pp. 85-90 (6 pages), Pittsburgh, USA, September 2010.
  12. Jonathan Weber, Sébastien Lefèvre,
    A multivariate Hit-or-Miss transform for conjoint spatial and spectral template matching,
    IEEE International Conference on Image and Signal Processing (ICISP), Springer-Verlag Lecture Notes in Computer Sciences, Vol. 5099, pp. 226-235 (10 pages), Cherbourg, France, August 2008.
  13. Anne Puissant, Sébastien Lefèvre, Jonathan Weber,
    Coastline extraction in VHR imagery using mathematical morphology with spatial and spectral knowledge,
    International Society for Photogrammetry and Remote Sensing Congress (ISPRS), 6 pages, Beijing, China, July 2008.
  14. Sébastien Lefèvre, Jonathan Weber, David Sheeren,
    Automatic building extraction in VHR images using advanced morphological operators,
    IEEE/ISPRS Joint Workshop on Remote Sensing and Data Fusion over Urban Areas (URBAN), 5 pages, Paris, France, April 2007.
Book Chapters
  1. Sébastien Lefèvre, Erhan Aptoula, Benjamin Perret, Jonathan Weber,
    Morphological Template Matching in Color Images,
    Advances in Low-Level Color Image Processing, Springer,pp. 241-277 (37 pages), 2013.
Editorial Activities in french
  1. Julien Longhi, Jonathan Weber,
    La communication numérique, du code à l'information, L'Harmattan, 2018.
Book Chapters in french
  1. Jonathan Weber,
    Enseigner l’informatique en DUT MMI : Difficultés et retours d’expérience,
    La communication numérique, du code à l'information, L'Harmattan,pp. 155-177 (23 pages), 2018.
Research Articles in National Journals
  1. David Sheeren, Sébastien Lefèvre, Jonathan Weber,
    La morphologie mathématique binaire pour l'extraction automatique des bâtiments dans les images THRS,
    Revue Internationale de Géomatique, numéro thématique "Informations géographiques : structuration, extraction et utilisation", Vol. 17, No. 3-4, pp. 333-352 (20 pages), 2007.
Communications to National Conferences and Workshops
  1. Bastien Latard, Jonathan Weber, Germain Forestier, Michel Hassenforder,
    Catégorisation d’articles scientifiques basée sur les relations sémantiques des mots-clés,
    Journées Francophones Extraction et Gestion des Connaissances (EGC), 2 pages, Paris, France, January 2018.
  2. Bastien Latard, Jonathan Weber, Germain Forestier, Michel Hassenforder,
    Utilisation des relations sémantiques des mots-clés pour la catégorisation d’articles scientifiques,
    Atelier Science des Données et Humanités Numériques (SDHN), Journées Francophones Extraction et Gestion des Connaissances (EGC), 12 pages, Paris, January 2018.
  3. Jonathan Weber, Sébastien Lefèvre, Pierre Gançarski,
    Segmentation vidéo interactive par zones quasi-plates,
    Colloque GRETSI sur le Traitement du Signal et des Images, 4 pages, Bordeaux, France, September 2011.
  4. Jonathan Weber, Sébastien Lefèvre, Pierre Gançarski,
    Zones quasi-plates spatio-temporelles et segmentation morphologique de séquences vidéo,
    Congrès des jeunes chercheurs en vision par ordinateur (ORASIS), 8 pages, Praz-sur-arly, France, June 2011.
  5. Jonathan Weber, Sébastien Lefèvre, Pierre Gançarski,
    Fouille vidéo orientée objet, une approche générique,
    Atelier Fouille de données complexes, Journées Francophones Extraction et Gestion des Connaissances (EGC), pp. 9-20 (12 pages), Brest, France, January 2011.
  6. Jonathan Weber, Sébastien Lefèvre, David Sheeren,
    Détection des bâtiments dans les images THRS avec la morphologie mathématique,
    Colloque International de Géomatique et d'Analyse Spatiale (SAGEO), 5 pages, Strasbourg, France, September 2006.
  1. Jonathan Weber,
    Segmentation morphologique interactive pour la fouille de séquences vidéo,
    PhD dissertation, 155 pages, Université de Strasbourg, France, September 2011.
  2. Jonathan Weber,
    Détection d’objets géographiques du littoral dans des images satellites multispectrales,
    Master dissertation, 60 pages, Université de Strasbourg, France, June 2007.
Other communications
  1. Jonathan Weber, Salvatore Tabbone,
    Localisation de symboles dans des documents techniques,
    Congrès National de la Recherche en IUT (CNRIUT), 1 page, Épinal, France, March 2015.
  2. Rachida Es-Salhi, Imane Daoudi, Hamid El Ouardi, Jonathan Weber,
    Co-segmentation des images : État de l’art,
    Journées Doctorales en Technologies de l’Information et de la Communication (JDTIC), Rabat, Morocco, March 2014
  3. Jonathan Weber, Sébastien Lefèvre, David Sheeren,
    Extraction automatique de bâtiments dans des images satellites THRS en utilisant des opérateurs de Morphologie Mathématique,
    Atelier du Programme de Télédétection Spatiale (PNTS), 1 page, Nantes, France, September 2007.