Data and Bioimage analysis

I am bioimage analyst, data scientist and R developer. I analyse biological images taken under the microscope using various image analysis software and I process the data I extract from them using the R software, for academic or private clients. I am instructor for image and data analysis. Finally, I am involved in the open source image analysis and R communities.

I was originally trained as an engineer in agronomy. Understanding complex systems, such as farming systems, requires knowledge from different fields, as well as the ability to discuss with people from various backgrounds in order to gather information, and the ability to train by oneself on new topics. This training gave me the opportunity to develop my ability to adapt to new situations and new issues, and gave me a strong taste for projects at the interface with several disciplines. To satisfy my curiosity toward fundamental biology topics, I then embarked for a PhD. Whereas the PhD is often seen as an overspecialization in a very focus domain, I had the chance to stay at the interface between physics and biology, work in a multi disciplinary team, and collaborate with scientist from other backgrounds. I developed my skills in biophysics, but also in microscopy, bioimage analysis, programming and statistics, applied to developmental biology. Developing organisms are complex systems, that are changing over time and space. They share common features, but each individual is unique. I have a particular interest for the assessment of spatio-temporal variability and robustness of development from image analysis and from multiple observations.

I like to share my research interests with other scientists from various backgrounds, as well as with a broader audience, from pre-school to adults. This blog is also a way of sharing science.


2019 - today: Application specialist for the Icy image analysis software. Bioimage Analysis Unit, Institut Pasteur, France.

2016 - 2019: Postdoctoral researcher. “Study of the morphogenesis of Arabidopsis thaliana lateral root using light sheet microscopy”. Ruprecht-Karls-Universität Heidelberg, Germany.

2016: Postdoctoral researcher (EMBO short term fellowship - 3 months). “Characterization of the cortical microtubules in the embryo of Arabidopsis thaliana”. Wageningen University & Research, Netherlands.

2012 - 2015: PhD on “Contribution of mechanical stress to cell division plane orientation at the shoot apical meristem of Arabidopsis thaliana”. ENS Lyon. France.


2016: EMBO Short term fellowship - 3 months.
2012: PhD grant from Région Rhônes-Alpes - 3 years.


2012 - 2015: ENS Lyon, Lyon. PhD thesis in Life sciences.
2011 - 2012: AgroParisTech, Paris. Master 2 degree in Plant sciences.
2009 - 2012: Agrocampus Ouest, Rennes. Engineering degree (= Master 2) in Agronomy.

Technical skills

  • Bioimage analysis ImageJ/Fiji, MorphoGraphX (3D segmentation), Ilastik (pixel classification), 3D meshes manipulation with R, Icy
  • Computational skills
    R and R Shiny language (3 R packages), ImageJ/Fiji macro language, git, GitHub, GitLab, CI, Linux, Bash, LATEX, Arduino, Matlab and Python notions.
  • Data analysis
    Generalized Linear Models, analysis of variance, multivariate analysis, geometric morphometrics and machine learning.
  • Microscopy
    Bright field, confocal (laser scanning and spinning disk) and light sheet microscopy
  • Biophysics
    IR and UV laser ablation, nano-indentation.

Interpersonal skills

  • Collaborations (with physicists (modelers and experimentalists), statisticians, computer scientists, spatial data analysts, and R developers)
  • Agile methodology and DevOps approach
  • Professionnal networks
    • Bioimage analysis: NEUBIAS
    • R programming: R Ladies remote, Grrr
  • Scientific communications (cf. publications)
    • 2 first authors and 1 review as first author
    • 2 co-authors and 1 reviews as co-author
    • International conferences (6 talks, 2 as invited speaker)
    • 3 R packages on my GitHub account
  • Training given
    • R programming language for beginners
    • Image analysis for beginners
    • Statistics for bachelor biology students
    • The cytoskeleton of Eukaryotic cells
    • French “qualification aux fonctions de maître de conférences”, section 66 and 65 (2018)
    • Co-organizer of NEUBIAS Training Schools number 10 and number 15
    • Co-organizer, moderator and instructor for the NEUBIAS Academy webinars
  • Supervision (6 students)
  • Outreach
    • Science festivals
    • Elementary and pre-school science education
    • Art & Science


For attribution, please cite this work as:
. (2020, Oct. 24). "About Marion Louveaux". Retrieved from

BibTex citation:
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    title = {About Marion Louveaux},
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    year = {2020}