The National Plant Phenotyping Infrastructure (NaPPI) was established to overcome the challenges in linking genotypes to phenotypes in fundamental and applied plant research. In this role NaPPI is advancing state-of-the-art Finnish plant science by providing access to specialized imaging instruments for monitoring plant growth, morphology and physiology, such as leaf temperature and photosynthesis, and by participating in phenomics data standardization at the European level. Furthermore, an effort is made to integrate phenomics data with molecular omics data, especially those of proteomics, transcriptomics and metabolomics data. NaPPI is a distributed research infrastructure currently with two nodes at UH and UEF that have complementing activities allowing wide range of phenotyping services to the research community across the country. Without access to high-throughput plant phenomics- metabolomics platforms, phenotyping by human eye is inaccurate, extremely slow and very labor-intensive. In combination with the phenomics and metabolomics services, the NaPPI installations provide a step towards bridging the gaps between whole-plant phenotypes of growth, development and physiology with integrated molecular profiles.

Contact details

Platform chair
Professor Pirjo Mäkelä,

Platform vice-chair
Professor Markku Keinänen, markku.keinä

Research coordinator
Dr Kristiina Himanen


Node/Host UniversityNode PI
Kristiina Himanen, UH
Markku Keinänen, UEF

UEF: University of Eastern Finland; UH: University of Helsinki; UO: University
of Oulu; UTU: University of Turku; TAU: Tampere University; ÅAU: Åbo
Akademi University.


The University of Helsinki (UH) node NaPPI has automated high-throughput plant phenotyping (HTPP) facilities with multiple RGBs, thermal imaging set-up and two chlorophyll fluorescence imaging units (Imaging PAMs) for small model plants (Compact system) as well as for large crop plants (Modular system), with capacities for 1080 and 270 plants, respectively. Automation of the plant management and movement to watering and imaging stations allows programming frequent actions thereby providing systematic data collection following plant performance. While HTPP generates large amounts of data, UH NaPPI has engaged with Phenomics data management utilizing the PHIS information system.

At the University of Eastern Finland UEF NaPPI has a wide range of specialized imaging instruments available at its Spectromics laboratory. The UEF NaPPI node houses five hyperspectral cameras covering the wavelength range from UV to midwave IR (250 – 5500 nm), liquid- cooled UV-optimized CCD (200 – 900 nm) and EMCCD cameras, light sources for fluorescence macroscopy, e.g. deep-UV LEDs, powerful and tunable narrowband light source, and three imaging PAMs. As part of the Academy of Finland’s Flagship programme on Photonics Research and Innovation (PREIN) and the UEF Center of Photonics Sciences the instrumentation of the UEF Computational Spectral Imaging group as well as their expertise in computational approaches is available for plant phenotyping purposes.

Recent user publications

Su et al., 2023. Tree architecture: Strigolactone-deficient mutant reveals connection between branching order and auxin gradient along tree stem. PNAS, 120;48.

Tenkanen, A, Suprun, S, Oksanen, E, Keinänen, M, Keski-Saari, S, Kontunen-Soppela, S 2021. Strategy by latitude? Higher photosynthetic capacity and root mass fraction in northern than southern silver birch (Betula pendula Roth) in uniform growing conditions. – Tree physiology 41: 974-991.

Pollari, M.; Sipari, N.; Poque, S.; Himanen, K.; Mäkinen, K. Effects of Poty-Potexvirus Synergism on Growth, Photosynthesis and Metabolite Status of Nicotiana benthamiana. Viruses 2023, 15, 121. DOI: 10.3390/v15010121

Hieta, J-P, Sipari, N, Räikkönen, H, Keinänen, M, Kostiainen, R 2021. Mass spectrometry imaging of Arabidopsis thaliana leaves at the single-cell level by infrared laser ablation atmospheric pressure photoionization (LAAPPI). – Journal of the American Society for Mass Spectrometry 32: 2895-2903.

Akinyemi, OO, Čepl, J, Keski-Saari, S, Tomášková, I, Stejskal, J, Kontunen-Soppela, S Keinänen, M. 2023. Derivative-based time-adjusted analysis of diurnal and within-tree variation in the OJIP fluorescence transient of silver birch. – Photosynthesis Research 157: 133-146.


Large UH NaPPI facility with trays and plants travelling autonomously between watering


imaging stations