Plant Imaging Unit

Sylvain Loubéry
Biologist and lecturer

+41 (0)22 379 65 68
Office 2065B
Sciences III

Anne Utz-Pugin

+41 (0)22 379 30 19
Lab 2065A


Research Interests

We develop new assays and analysis pipelines for plant biology using our expertise in various microscopy fields: fluorescence microsopy, histology, transmission and scanning electron microscopy and image analysis. We apply our skills to all the model systems studied in the Botany and Plant Biology Department (Arabidopsis seeds, seedlings and adult plants, tobacco and rice, protoplasts, algae, etc.).




Topographic and histochemical colorations on fresh vegetal material (free-hand or vibratome sections) or fixed and included material (microtome slices).


Fluorescence microscopy


Use of widefield and confocal imaging for the observation of fluorescent proteins or markers in cells in culture (protoplasts, unicellular algae such as Chlamydomonas) or in tissues or seedlings of tobacco or Arabidopsis.

Immunofluorescence stainings on Arabidopsis seedlings and unicellular algae.



Electron microscopy


Scanning electron microscopy to observe surface structures on various types of plants, on fresh material or on fixed organs treated with critical point drying.

Transmission electron microscopy for the visualisation of the ultrastructure of unicellular algae, seeds and various Arabidopsis tissues.



Image treatment and analysis


ImageJ, Photoshop and Illustrator for the treatment and mounting of pictures, and writing of ImageJ macros.


In situ hybridisation on Arabidopsis embryos is currently being developed in our unit.


We offer our skills in microscopy to:

  • Conceive and plan experiments ;
  • Prepare samples and acquire images ;
  • Treat and analyse pictures.

These services are offered as collaborations with the different laboratories of the Department of Botany and Vegetal Biology, among others.

Another of our objectives is to develop novel approaches and methods for plant imaging.

In addition, we train users on various kinds of microscopes, and maintain the microscopy equipment of the Department of Botany and Plant Biology (widefield microscopes and stereomicroscopes).



Course 12B013: Plant biology

Mandatory course for 2nd-year bachelor students in biology.

This part of the course consists in 12h of lecture and 3 afternoons of practicals dedicated to the study and the observation of the different vegetal tissues and organs.


Course 14B640 : Histology and tissue imaging

Optional course for 3rd year bachelor and master students.

Theoretical and practical course covering classical histology techniques, as well as confocal imaging and image analysis (40h in total).

CUSO course: Plant imaging: advanced light microscopy

2-days intensive course for PhD students.

Lectures and hands-on sessions covering the preparation and the observation of plant samples by optical microscopy, as well as basic image analysis.


Course 14B063A: Microscopy and imaging

Optional course for Master and PhD students and post-docs.

Lectures and hands-on sessions covering basic and advanced fluorescence imaging.


Course 14B044: Electron microscopy

Optional course for Master and PhD students and post-docs.

Lectures and hands-on session covering the preparation and the observation of samples by transmission and scanning electron microscopy.


Supervision of Bachelor monographies.


Key Publications

Loubéry S., De Giorgi J., Utz-Pugin A., Demonsais L. & Lopez-Molina L.: A Maternally Deposited Endosperm Cuticle Contributes to the Physiological Defects of transparent testa Seeds.
Plant Physiol 2018, 177(3):1218-1233. PMID: 29848749.

Yin R., Skvortsova M.Y., Loubéry S. & Ulm R.: COP1 is required for UV-B-induced nuclear accumulation of the UVR8 photoreceptor.
Proc Natl Acad Sci U S A 2016, 113(30):E4415-22. PMID: 27407149.

De Giorgi J., Piskurewicz U., Loubery S., Utz-Pugin A., Bailly C., Mène-Saffrané L. & Lopez-Molina L.: An Endosperm-Associated Cuticle Is Required for Arabidopsis Seed Viability, Dormancy and Early Control of Germination.
PLoS Genet 2015, 11(12):e1005708. PMID: 26681322.

Lefebvre-Legendre L., Choquet Y., Kuras R., Loubéry S., Douchi D. & Goldschmidt-Clermont M.: A nucleus-encoded chloroplast protein regulated by iron availability governs expression of the photosystem I subunit PsaA in Chlamydomonas reinhardtii.
Plant Physiol 2015, 167(4):1527-40. PMID: 25673777.

Colinas M., Shaw H.V., Loubéry S., Kaufmann M., Moulin M. & Fitzpatrick T.B.: A pathway for repair of NAD(P)H in plants.
J Biol Chem 2014, 289(21):14692-706. PMID: 24706747.



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