Update and face-lift coming soon :)!

It has been hectic and our website is badly needing an update. We will try our best to do that in the near future, apologies! In short, we now have three new ongoing projects  funded by the Academy of Finland (see below), which means we also have some new faces, collaborators and new exciting research, stay tuned!

  • Sensing plant Biogenic Volatile Organic Compounds (SensBVOCs), 2021-2024 (PI, Chao Zhang). The project investigates and models the spectral expression of  BVOC emissions and their dynamics.
  • Mechanistic remote sensing of forest climate impacts (MONOCLE), 2022-2027 (PI, Jon Atherton). The project investigates how climate impacts on forests reflect on remote sensing data and how this information scales from the leaf to the satellite pixel.
  • Resolved optical ecophysiology: leaf level (REDEYE), 2022-2026 (PI, Porcar-Castell).  The project develops and implements novel protocols combining gas exchange, spectral reflectance and fluorescence to resolve and model the regulation of photosynthesis in situ. Currently hiring a PhD student! you can look and apply here


Winter Update (2019/2020): Optics of Photosynthesis Lab

Dear all, here comes our next Lab update!

Certainly the most prominent news from the last months has been our unprecedented  peak in productivity. Big congratulations to Paulina and Jon for their respective new family members :D!

Congratulations also to Shari for her recently published paper in Photosynthesis Research which reveals the wealth of information that can be tapped from investigating the kinetics of the reflectance and transmittance spectra of leaves upon a light induction. The Open Access paper (courtesy of University of Helsinki) can be
accessed via this link. In addition we are currently working with multiple papers from our past FAST 2017 boreal forest campaign, 2018 potato crop campaign, long-term Monitoring PAM datasets, as well as a perspective paper from our FAST 2019 Workshop. Hopefully we can add more details and links in next update :)!

Last but not least, our Academy of Finland FLUOSYNTHESIS project is coming to an end in August 2020 which means we are actively seeking for new sources of funding to continue (and expand!) our Lab activities to different research areas. Our mission and vision statements remain however untouched… we will continue striving to interpret the information embed in the light emitted or reflected from plants.

South view from Mount Caro (1441m, Spain). Photo: Albert Porcar-Castell (In the far left corner are the grounds where I used to play as a child)

Spring/Summer Update (2019/II): Optics of Photosynthesis Lab

OK, perhaps we were too optimistic… let’s say we will try to provide a quadrimestral update of Lab activities :). So what happened of late:

1/ Based on discussions during the recent FAST Workshop. We decided to establish and host the SIF-community mailing list. The list has now over 175 members from across the globe and can be used to disseminate papers, job adds, post SIF-related questions, etc… to subscribe you just need to send an email to majordomo@helsinki.fi with the following text: “subscribe SIF-community and-your-email-address”. You can also find further information in this link

2/ Publications: We have got a few great papers recently accepted and/or published!

In Atherton et al (2019) we present a new method to measure the full fluorescence spectra of plant canopies (e.g. a forest stand) in situ. You just need a powerful disco light! Furthermore, in Liu et al (2019) we assess the factors that contribute to the top-of-canopy fluorescence emission by combining the realistic 3D structure of a birch stand with ample empirical measurements. Both these papers are published open access in Remote Sensing of Environment. More recently, in Zhang et al (2019) we show how all fluorescence wavelenghts are capable of conveying the spring recovery of photosynthesis in evergreen Scots pine needles. Still, changes in the spectral shape, although small, can be highly informative!

3/ We recently conducted a small campaign here in Helsinki to collect a few more functional/optical/biochemical properties of boreal species. This data is to contribute to a future meta-analysis…we are just missing a few tropical species now 🙂

4/ Ongoing: We are working on a couple of our papers related to our 2018 Potato experiments, MoniPAM papers, drone SIF papers and of course preparing for Funding application rounds in September. Don’t forget to follow us on twitter too @Optphotolab

  (View to the Baltic Sea from Valli island, Vallisaari. Photo: Albert Porcar-Castell)

Summer regards from OPL!

Winter Update (2019/I): Optics of Photosynthesis Lab

We recently decided to provide a trimestral update of our Lab activities, here comes the first summary covering the past winter months:

FAST 2019 workshop:
During February 25-March 1st OPL hosted the 1st FAST Workshop (Fluorescence Across Space and Time) in Hyytiälä Forest Station. A total of 35 participants from 10 different countries and from very diverse backgrounds (from nanosciences to global land surface modelling) joined the Workshop to discuss and brainstorm on current challenges and opportunities of SIF across scales. Thank you all for making the effort of coming to Hyytiälä! We hope we can turn the outcome of the Workshop into an Opinion paper, so stay tuned!

New papers in “Remote Sensing” Journal:

1) Paulina recently published her first article “Leaf-level spectral fluorescence measurements: Comparing methodologies for broadleaves and needles”  (DOI:10.3390/rs11050532). In this study we compared three different methodologies for measuring reflectance and fluorescence of leaves and (especially) needles! We argue that needle mats, despite of potentially enhancing red fluorescence reabsorption, are an advantageous solution to track the seasonal changes in fluorescence spectral properties of needles.

2) Hyytiälä was probably (“one of” or “the”) first site to start monitoring canopy spectral reflectance and solar-induced fluorescence (SIF) back in 2010 with Dr. Caroline Nichol from the University of Edinburgh. A few years later, we are very happy to see the first SIF article published “Diurnal and seasonal solar induced chlorophyll fluorescence and photosynthesis in a boreal Scots pine canopy” (DOI: 10.3390/rs11030273). The paper reports only a modest correlation between SIF and photosynthesis for the evergreen forest. Inherent challenges are discussed and a new scheme for SIF normalization introduced.

Welcome Dr. Shari Van Wittenberghe!
Shari recently joined OPL as a visiting scientist and will stay with us for the next year as part of her Postdoctoral Fellowship (See Who we are section). Among other things, Shari will be investigating the mechanisms that control the short-term responses of reflectance, transmittance and fluorescence in leaves with different states of down-regulation.

Currently working on: Processing chain for Monitoring PAM data, drone SIF, potato fluorescence, FAST campaign publications, Nocturnal LEDIF (First paper currently in Press in RSE),…

Next update: June 2019

Beñat Olascoaga defended his PhD Thesis

MSc. Beñat Olascoaga defended his PhD thesis on 9.3.2018 at the Department of Forest Sciences “Leaf optical properties and dynamics of photosynthetic activity”. The summary part of the Thesis can be found in the link below:


Congratulations to the new Doctor! We wish Beñat all the success in his new postdoctoral stage!

Optics of Photosynthesis Lab contributes to the observation of photosynthesis from Space

Over the last decade, a few space missions have shown that the tinny chlorophyll fluorescence signal that emanates from all higher plants can be seen from space. These missions however had very coarse resolutions (with e.g. 100km2 pixels) which greatly limited their scientific utilization.

OCO-2 is one of NASA’s new satellites from which solar-induced fluorescence (SIF) can be retrieved whithin a Fraunhofer line located around 760nm. In a recent Science paper, Sun et al. demonstrate the new capabilities of OCO-2 derived SIF which, at a spatial resolution of 1×2 km, can already yield meaningful SIF values that show particulartly good correlations with tower-based measurements of gross primary productivity. In  this study we assess the future potential and challenges for the interpretation of SIF data sources that are continuously increasing in quality and resolution. In this context, OPL is currently working towards the mechanistic understanding of multiscale SIF drivers, in preparation for future hi-resolution satellite data. See Full PDF in our Publication Section.

Background Spatial variation in key leaf optical traits controlled by light environment and species

Remote Sensing acquires optical data across space and time. We then want to interpret the data in terms of spatial and temporal variation in plant functional or biochemical traits. In a recent paper (Atherton et al. 2017, see publications) we investigated the background spatial variation in key optical properties/traits like the photochemical reflectance index or the shape and intensity of the leaf chlorophyll fluorescence spectra and  the factors that control it. We found that both the light environment within plant canopies and the species generate background spatial variability in the above optical traits which needs consideration when interpreting remotely sensed data.


New Lab Member

Anu Riikonen has recently joined our Lab. She just finished her PhD studies and will help us coordinating the project “Cost-effective methods for tracking large scale vegetation physiology (see projects)”.  We will certainly benefit from her expertise with field ecophysiological measurements and stakeholder interaction.

Welcome Anu!

By the way, Anu will also give a hand with the website so it probably start to look gradually better 🙂


The Optics of Photosynthesis Lab gets Key Funding from the Academy of Finland

Cost-effective methods for tracking large scale vegetation physiology: Participatory phase and pilot experiments

Society faces the challenge of an increasing population that concentrates in urban areas. Food production needs to be increased following sustainability criteria for optimal use of water, fertilizers and pesticides. Air pollution and human stress are an increasing problem in urban areas which could be also improved through detailed management and expansion of urban forests and parks. These challenges require new and cost-effective tools to track the health status of vegetation.

With the advent of unmanned aerial vehicles (UAVs) and hyperspectral imaging systems it might be now possible to acquire detailed information on vegetation health and physiological status anywhere and anytime. In this project we will evaluate the potential of advanced optical indices (emission of chlorophyll fluorescence and other fine variations in vegetation reflectance) to monitor vegetation health using UAVs. We will conduct pilot campaigns both in city parks as well as in farms. Stakeholders include: the City of Helsinki,  the Finnish Geospatial Institute, the Natural Resources Institute of Finland, as well as private partners from the hyperspectral sensor industry and agricultural sectors.

See more details in the Section PROJECTS