Root Phenotyping Platform


The Root Phenotyping Platform, created in 2017, is hosted by the « Institute for Plant Sciences of Montpellier » department. It is dedicated to kinetic and non-destructive analysis of seedling Root System Architecture of many species including Arabidopsis, rice, tomato, rapeseed, and Medicago grown in vitro. The main objective of the platform is to develop approaches, tools and methods to characterize the impact of different growth environments on root growth and development. This includes osmotic stresses, nutrient deficiency or excess or biotic interactions alone or in combination. These analyses provide the basis for further genetic and molecular physiology approaches.

Seedling are grown in vitro on 120x120mm (Small plates: SP) or 245x245mm (Large plates: LP) Petri dishes. The phenotyping facility includes a self-contained imaging unit that can handle up to 72 LP and 200 SP at once with imaging frequency ranging from 2 to 24 hours.

The imaging automat is located in a dedicated growth chamber allowing temperature, hygrometry, photoperiod, light intensity being adjusted according to user’s requirements.


It is equipped with a 16Mpixel linear camera, a telecentric objective and collimated LED backlight for images at 10µm resolution with high contrast (even for thin and almost translucent Arabidopsis roots).

Collected images are stored on long term on a secure data storage system.

Images are analyzed through semi-automated or fully automated pipelines integrated in the OpenAleaLab suite ( The Root Phenotyping Platform is backed to B&PMP research programs but is open to the scientific community through local, national and international collaborations

  • Access to the phenotyping platform is through scientific collaborations.
  • Applications should be done via the « Application form » and emailed to Applications will be evaluated by the platform steering committee. Once a decision has been notified, get in touch with Philippe Nacry for organizing the schedule and experiments.
Non destructive and kinetic analysis of root system architecture of seedlings from various species grown in vitro.
Equipment / Technologies
  • Dedicated growth chamber
    • Temperature (12 to 35°C),
    • Hygrometry (50% to 95%),
    • Lighting: Vegeled Floodlight (40 to 350 µE)
    • Photoperiod from 0 to 24H


  • Imaging automate
    • 72 large plates (240x240mm) or 200 small plates(120x120mm)
  • Safe 50To data storage system
  • Dedicated Image analysis working station
  • Providing assistance to users, including technical assistance for the design of the monitoring of the experiment,
  • Full access to IPSiM facilities for medium preparation clean benches for in vitro culture.
  • Management and secure storage of data
  • User training

Assistance and advices for image analysis


Fernandez R, Crabos A, Maillard M, Nacry P, Pradal C (2022) High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings. Plant Methods, 18(1):127

Berger N, Demolombe V, Hem S, Rofidal V, Steinmann L, Krouk G, Crabos A, Nacry P, Verdoucq L, Santoni V (2022) Root membrane ubiquitinome under short-term osmotic stress. Int. J. Mol. Sci., 23(4):1956

Kupcsik L, Chiodi C, Moturu TR, De Gernier H, Haelterman L, Louvieaux J, Tillard P, Sturrock CJ, Bennett MJ, Nacry P, Hermans C (2021) Oilseed rape cultivars show diversity of root morphologies with the potential for better capture of nitrogen. Nitrogen, 2(4):491-505

Smokvarska M*, Charbel F*, Platre MP*, Fiche J-B, Alcon C, Dumont X, Nacry P, Bayle V, Nollmann M, Maurel C, Jaillais Y, Martinière A (2020) A plasma membrane nanodomain ensures signal specificity during osmotic signaling in plants. Curr. Biol., 30(23):4654-4664.e4