Plant spectral imaging and phenotyping laboratory

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Plant spectral imaging and phenotyping laboratory (formerly Spectromics laboratory) forms together with the University of Helsinki the Finnish National Plant phenotyping Infrastructure (NaPPI), that belongs to the Biocenter Finland. Laboratory is part of the UEF Center for Photonics Sciences and Research Council of Finland’s Flagship on Photonics Research and Innovation (PREIN).

Cooperation

Research equipment

Specim sCMOS V10E VNIR (400 – 1000 nm)
Specim SWIR (1000 – 2500 nm)
Specim MWIR (3000 – 5000 nm)
Specim IQ portable VNIR camera (400 – 1000 nm)
Headwall UV (250 – 600 nm)
IMEC VNIR Snapscan (470 – 900 nm)
Imaging pulse-amplitude modulated fluorometers
PSI FluorCam FC-800
PSI Handycam

Non-imaging pulse-amplitude modulated fluorometer
PhotosynQ MultispeQ v.2.0 (battery-operated, portable, 2x)

Rapid fluorescence transient (OJIP) fluorometer
PSI PAR-FluorPen FP 110/D (battery-operated, portable, 2x)
FLIR E8
FLIR C3
Nikon D610
Nikon D7000 (modified camera, UV-only, 300 – 400 nm)
– UV macro Nikon Rayfact 105/4.5
Nikon D7000 (modified camera, visible + infrared (400 – 1000 nm)
Several Nikkor-objectives
Canon EOS 650D + EF 100 2.8L Macro IS USM + macro ring lite MR-14EX
Leica Z6 APO + Leica DFC450 C (motorized zoom-macroscope)
Zeiss Axioscope A1 (fluorescence microscope)
Andor Zyla sCMOS
Andor iXon Ultra 888 EMCCD
Andor iKon-M (UV + VIS, 200 – 1000 nm)
Spectral camera IMEC Snapscan (470 – 900 nm)
Sutter Instruments Lambda LS Xenon light source with adjustable narrow-band (15 nm FWHM in 1 nm steps) angle-tunable thin-film interference filters and liquid light guides (338 – 700 nm + IR)
Selection of UV and VIS LEDs
Various halogen lamps
Battery-operated UV torches
Dualex Scientific+, battery-operated instrument for chlorophyll, flavonol and anthocyanin contents

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Plant spectral imaging and phenotyping laboratory

Cooperation

Research equipment

Spectral cameras

Chlorophyll fluorescence measurement

Thermal cameras

DSLR cameras

Microscopes and microscope cameras

Light sources

Other optical devices and components

Keywords

Personnel

Markku Keinänen

Sari Kontunen-Soppela

Leah Marie Martin

Observing accelerated chemical colour change in aspen and birch wood using hyperspectral imaging and spectrophotometry

Short-term effects of low-intensity surface fires on dissolved organic matter from boreal forest soils

Advancing hyperspectral imaging techniques for root systems: a new pipeline for macro- and microscale image acquisition and classification

Day-to-day variation in chlorophyll fluorescence parameters of northern and southern silver birch in a common garden

Hyperspectral imaging for identification of irregular-shaped microplastics in water

Derivative-based time-adjusted analysis of diurnal and within-tree variation in the OJIP fluorescence transient of silver birch

Detection and identification of microplastics directly in water by hyperspectral imaging

Making the Genotypic Variation Visible: Hyperspectral Phenotyping in Scots Pine Seedlings

Polar day syndrome: Differences in growth, photosynthetic traits and sink-size patterns between northern and southern Finnish silver birch (Betula pendula Roth) provenances in native and non-native photoperiods

Assessment of a portable UV-Vis spectrophotometer's performance in remote areas: Stream water DOC, Fe content and spectral data

Mass Spectrometry Imaging of Arabidopsis thaliana Leaves at the Single-Cell Level by Infrared Laser Ablation Atmospheric Pressure Photoionization (LAAPPI)

Assessment of a portable UV-Vis spectrophotometer's performance for stream water DOC and Fe content monitoring in remote areas

Differences in growth and gas exchange between southern and northern provenances of silver birch (Betula pendula Roth) in northern Europe

Identification of peat type and humification by laboratory VNIR/SWIR hyperspectral imaging of peat profiles with focus on fen-bog transition in aapa mires

Spectral Reflectance in Silver Birch Genotypes from Three Provenances in Finland

Strategy by latitude? Higher photosynthetic capacity and root mass fraction in northern than southern silver birch (Betula pendula Roth) in uniform growing conditions

Fotoniikasta valoa Suomen hyvinvointiin: Selvitys alan vaikuttavuudesta ja kasvunäkymistä

Kohti virtuaalisuutta kasvibiologian opetuksessa

Leaf Canopy Layers Affect Spectral Reflectance in Silver Birch

Narrowband-autofluorescence imaging for bone analysis

Automated image analysis tool to measure microbial growth on solid cultures

Genotype- and provenance-related variation in the leaf surface secondary metabolites of silver birch

Imaging lichen water content with visible to mid-wave infrared (400 - 5500 nm) spectroscopy

Intrapopulation genotypic variation in leaf litter chemistry does not control microbial abundance and litter mass loss in silver birch, Betula pendula

Nordic research infrastructures for plant phenotyping

Transcriptional effects of cadmium on iron homeostasis differ in calamine accessions of Noccaea caerulescens

Intrapopulation Genotypic Variation of Foliar Secondary Chemistry during Leaf Senescence and Litter Decomposition in Silver Birch (Betula pendula)

Low vapor pressure deficit reduces glandular trichome density and modifies the chemical composition of cuticular waxes in silver birch leaves

Thermal and hyperspectral imaging for Norway spruce (Picea abies) seeds screening

Natural Vision Data File Format as a New Spectral Image Format for Biological Applications