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Using R for photobiology ISSN 2343-3248 (Helsinki, Finland)

  • ggspectra 0.3.10
    by Pedro J. Aphalo on 2023-01-15

    This update to ‘ggspectra’ tracks changes in ‘photobiology’ 0.10.15, ‘photobiologyWavebands’ 0.5.1 and ‘ggplot2’ 3.4.0, as well as in R 4.1.0. These are mostly deprecations that would trigger warnings. Please, be aware that these versions or later are now required. The corrected definition of PAR() in ‘photobiologyWavebands’ 0.5.1 is code breaking as this change will cause some plots, especially annotations in them to change, when PAR() has been explicitly called in users’ code for quantities that are not photon based, in... Continue reading

  • photobiologyWavebands 0.5.1
    by Pedro J. Aphalo on 2023-01-05

    PAR, or photosynthetically active radiation, as defined by McCree (1972) and used almost universaly in plant sciences is a biological spectral weighting function or BSWF that for spectral irradiance in photon based units takes one of two values for the weights: 0 or 1. So for computations of PAR photon irradiance (or PPFD) it is equivalent to integration over a range of wavelengths without application of a weighting function. However, PAR, as defined by McCree, has a BSWF with weights... Continue reading

  • photobiology 0.10.15
    by Pedro J. Aphalo on 2023-01-04

    One of the features of the package for a long time has been automatic wavelength interpolation when needed in computations involving two spectra. However, until the current version this behaviour did not extend to operations summarizing multiple spectra stored as members of the same collection, as inconsistent wavelength values triggered an error. This update to ‘photobiology’ enhances the compatibility of ‘ggspectra’ with spct objects that have been reduced in size by removal or “thinning” of intermediate wavelength values in rectilinear... Continue reading


Canopy Spectral Ecology and Ecophysiology Matthew Robson's Research Group Pages

  • Functional role of aquaporins models plant to beech trees: David Israel’s PhD defence
    by Matt on 2023-01-21

    The public PhD defence of David Israel is on Friday 27th Jan 2023 13:15-15:15 EET with opponent Oliver Brendel from INRAE at Nancy, France. David Israel: The ecophysiology of plasma membrane aquaporins in Arabidopsis thaliana and Fagus sylvatica Biokeskus 2, auditorio 1041, Viikinkaari 5 This research makes the connection from expression of aquaporins in plant … Continue reading "Functional role of aquaporins models plant to beech trees: David Israel’s PhD defence"

  • Research overview
    by Matt on 2023-01-20

    This 12 minute video gives a simple introduction to our research into: (1) how plant canopies use and filter the sunlight that they receive; (2) what happens under an overcast or clear sunny sky; and (3) a beech provenance trial in Helsinki. https://unitube.it.helsinki.fi/static/mh_default_org/api/cf8af451-a0f4-4f8e-ac07-d953f452c6a7/947adf59-b621-4c36-962b-6d6a55d79ef9/OEBDay.mp4

  • A walk in the woods
    by Matt on 2023-01-15

    Relive a spring afternoon in Viikki Arboretum, Helsinki,  just as the trees are coming into leaf. Janne Halme and Bart Vandeput chat with me about forests and their use of light for the Painting Energies Podcast  below.    


Sensory and Physiological Ecology of Plants Decoding the acquisition and use of information by wild and cultivated plant species

  • The Earth is not flat. Are plants and plant canopies flat?
    by Pedro J Aphalo on 2022-12-30

    The problem Irradiance or spectral irradiance on a horizontal plane is normally used to quantify energy or photons available for photosynthesis. Similar measurements of irradiance in narrow bands of the spectrum or spectral irradiance measurements are used to characterize radiation features perceived by plant through photoreceptors. In the case of photosynthesis this makes some sense … Continue reading "The Earth is not flat. Are plants and plant canopies flat?"

  • Visit to Universidad Austral de Chile
    by Pedro J Aphalo on 2022-12-22

    I recently visited Universidad Austral de Chile (UACh) located i n Valdivia. This trip is part of a colaboration with Daniel Calderini in a project about responses of wheat to planting density. My contribution is related to light quality in wheat canopies with plants at different spacing. I also taught an intensive doctoral course titled … Continue reading "Visit to Universidad Austral de Chile"

  • The R Universe
    by Pedro J Aphalo on 2022-12-18

    My R packages are now listed at the R universe, a new web site with a repository of packages accesible in multiple ways.  It is implemented as a database rather than being static like CRAN. The R Universe seems like a good tool to not only find packages but also to monitor their health. Its … Continue reading "The R Universe"


Photo rumblings and whispers Techniques, equipment, approaches, commentaries and more

  • Notes on OM System OM-1 digital camera (DRAFT)
    by Pedro J. Aphalo on 2022-12-29

    Quite a lot has been already written in the internet about the OM System’s OM-1 camera, but I write down here some notes comparing it to the E-M1 Mk II and highlighting some use cases. I share this notes in case someone else finds them useful, although they are mostly intended for myself. Among the things frequently mentioned is a lack of improvement in image quality between old and new image sensors (e.g., OM system OM-1 vs OM-5 – The 10 Main Differences). This is one example of where my own experience differs drastically from the quick and dirty tests... Continue reading

  • Small Fill/Video LED lights revisited
    by Pedro J. Aphalo on 2022-10-15

    Four years ago I wrote a post comparing the Sunwayfoto Fill Light FL96 and the Aputure Amaran AL-M9 mini LED light. They are both still available new. Sunwayfoto has released a few variations on the original model, the FL96 C with batteries with increased capacity and faster chargin through USB-C, and in the case of the FL120, slightly higher light output and power-bank function. A few days ago I bought an Elgato Key Light Mini, and decided to run a new and more thorough comparison between these the three commercial LED light sources that I own. In part because I... Continue reading

  • Broad band VIS+NIR LEDs
    by Pedro J. Aphalo on 2021-10-25

    Broadbands LED based on a blue LED and “phosphors” have appeared in the market. One example is type SMB1N-BB450 from Roithner LaserTechnik (Vienna, Austria). The primary LED has a peak of emission at 450 nm and the spectrum as a whole covers the range 400 nm to 1000 nm. Except for the prominent blue peak the spectrum is rather flat, making it useful light source for VIS and specially NIR imaging and spectrometry. This LED type seems useful for photography as well as for its intended use is spectrometry. Emission is rather weak and efficiency rather low, emitting 0.3W of... Continue reading

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