Development of hardware, software and protocols

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People

  • Pedro J. Aphalo, PhD, Docent (University of Helsinki)
  • Collaborators
  • Nikolai Belevich, PhD (Institute of Biotechnology, University of Helsinki)

Aim and objectives

The aim of this work is sometimes to make certain experiments possible. In other cases it has to do with making some methods and protocols more easily accessible to other researchers. Occasionally it has been driven by the need to use cheaper equipment.

Background

Software: I have been developing software since the end of the 1970’s. I have developed statistical software, simulation models, a library for simulation modelling, software for controlling experiments (e.g. a modulated UV supplementation system). I have also developed software for controlling a proprietary gas-exchange system, and I am developing software for control and data acquisition with a spectrometer. I have have programmed in more than 10 different computer languages. I also designed software for quantification of roots in minirhizotron images (https://bitbucket.org/aphalo/rootview).

Hardware: I have designed and built and electronic auxanometer, digital thermometers, three-state temperature controllers and power electronics for controlled environments. Modified a gas-exchange system and a transient porometer.

Current

Software: I am developing software for diverse calculations related to photobiology and and quantification of radiation. There is a separate web site for this software at http://r4photobiology.wordpress.com/. Thirteen of my packages are available through CRAN. I am writing companion book for these software packages. Its drafts is available at Leanpub.

Hardware: Design and assembly of special LED light sources and drivers for use in our experiments. I have collaborated with Aralab in the customisation of light sources in growth chambers and I am collaborating with sglux by testing a prototype spectrometer. Acquisition and specification of equipment for UV, VIS, NIR, and thermal imaging, including cameras, objectives, filters, and manual and mechanised support systems. More information about photographic techniques including imaging in the near ultraviolet- and near-infrared regions with modified and off-the-shelf digital cameras is available at my web site on the subject Photo rumblings and whispers. Current work in progress on low cost miniature narrow-band- and multispectral radiation sensors with autonomous logging capabilities.

Information and disemination on methods: Currently through the UV4Plants Association, as information officer and editor-in-chief of the UV4Plants Bulletin. I am also the lead author of a book on Using R for Calculations Related to Photobiology. Earlier through participation in COST Action FA0906, mainly in the work group on UV technology, we have co-organised training schools and and co-edited a handbook of methods titled Beyond the Visible. See the UV4Plants web site for more details.

Published software

R for Photobiology Suite of packages

RootView root tracing in minirhizotron and rhizotron images.

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