Photo-spectrum Services

Photobiology-Research Consulting

Pedro J. Aphalo "Photo Spectrum Services" — Wed, 11 Nov 2026 22:00:00 GMT

Experience

I have authored and coauthored more than 100 scientific publications, most of them related to plant photobiology. Designing, supervising and working in these many and varied experiments I have gained broad experience on avoiding and solving different problems. During my career I have regularly designed and built new equipment to make novel studies possible. Techniques for manipulation and measurement of illumination in effective ways have been one of my interests. I was the lead editor of a handbook of methods in photobiology. I have developed R software for various photobiology-related computations as well as software for spectral data acquisition. Earlier I have developed software for control and measuremt with a custom-built gas-exchange system, and well as simulation models. I have also experience in the customization, modernization, use and specification of requierements for growth chambers and growth rooms.

Consulting on light measurement

I do not own equipment for light measurements. However, I have long experience in their use. I can advice and provide training on the measurement of both natural and artificial light sources, in the UV, VIS and NIR wavelengths. This includes the calculation of the different summary quantities like PAR, photon ratios and Pfr:Ptot and the various inconsistent definitions in common use or their suitability for different applications. I am also familiar with many of the light measurement instruments used in agricultural meteorology as well as in controlled environments, both broadband and spectral.

Consulting on light manipulation

Mechanisms behind plant responses to illumination are complex. Treatments can easily have side effects that need special consideration when designing experiments to study plants’ responses to illumination. In addition when designig experiments it is necessary to be well informed about currently available light sources and light control approaches. Advances in electronics and LED technology are not only important for plant cultivation but can also create new possibilities for research. Even things that are well know in the electronics and photonics fields can remain out of reach of photobiologist, because of difficulties in communication or simply lack of time to explore new technologies. I can help with these problems as because of my experience I am able to communicate across disciplines.

Even if I am far from being an expert in illumination or electronics, I know enough to be able to effectively discuss requirements of biologists’ experiments in terms that an engineer can understand. I have succesfully played this role in research projects that involved both plant biology and electronic engineering and illumination.

Consulting on plant photobiology and plant ecophysiology

Design of experiemnts

I can help design experiments in these fields, both from a statistical perspective and the practicalities of planning. This is vast field, and depending on the case, I may be able to advice on even subtle details and warn about common pitfalls.

Instrumentation

I have long experience not only of buying standard equipment but also discussing unique customizations to standard equipment, having special custom equipment made, and even of designing and building control equipment for experiments. I am also likely to be able to help finding the most suitable and cost-effective instruments and equipment, suppliers and service providers. Not only because I have experience in their use but also because I have experience in reading technical specifications and discussing them with suppliers.

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Technical Photography Services

Pedro J. Aphalo "Photo Spectrum Services" — Sat, 06 Jun 2026 21:00:00 GMT

Services

I have long-time experience both in every day photography and in specialised techniques. I have been actively taking photographs since I was nine years old. As a university undergrad I started using photography as a tool for my research and scientific endeavours to this day while remaining also a serious hobby.

“Small” subjects: Macro photography of plants, insects, and electronic circuits and components are my most frequent subjects. I use both single-image- and multi-image techniques such as focus-stacking, sensor-shift high-resolution and multi-image averaging.
“Narrow” and far-away subjects: Use of telephoto lenses for bird photography in the natural environment, and occasionally plants and plant parts. In combination with close-focusing, photography of insects in the wild.
“Normal” subjects: Use of normal, noderate telephoto and moderate wide angle lenses for landscapes, cityscapes, various types instrumentation, research facilities, individual and groups of plants under study, etc.
“Wide” subjects: Use rectilinear and circular (fish-eye) wide angle lenses for open landscapes as well as characterization of vegetation structure and its influence on understory illumination.
Near-infrared (NIR): Using a full-spectrum-modified camera together with long-pass optical filters I photograph reflected near infrared radiation. I use this approach for the different types of subjects described above.
Ultraviolet-A1 (UV-A1): Using a full-spectrum-modified camera together with short- and band-pass optical filters I photograph plants, lichens, mushrooms and landscapes. The types of subjects are constrained by the need to use special lenses. I have suitable macro and normal lenses.
Autofluorescence: This is photography of longer-wavelength light emitted by subjects when illuminated by visible light or UV-radiation of shorter wavelengths. As intensity of the emitted fluorescence is much weaker than that of the light used for excitation, very good filters are needed to discriminate between them. It is also necessary to use strong illumination as excitation. This limits the use of this technique to subjects not more than a few meters from the camera under artificial illumination. In the field it can be used only in the dark of the night.
Multi-image methods: The cameras I use have built-in support for focus stacking, sensor-shift high resolution, and image-averaging. The merging of these images can take place in-camera or in post-processing. In the case of multi-image panoramas that extend the field of view, I rely on alignment and merging during post processing while in the case of sensor-shift high-resolution images, I always rely on in-camera merging into high resolution RAW files.
Digitizing: Camera-based digitising of colour and black-and-white film negatives and of colour slides is nowadays the preferred approach, with only the very best film scanners providing better bit depth.
Spectral imaging: I am developing a system for illumination-based spectral photography of small objects. I have now built a computer-controlled LED-driver with 16 channels. Each channel can dimmed by either constant-current or pulse-width-modulation, or both approaches combined. With custom-assembled 120 W LED arrays it is possible to have 12 different colors in the same light source and switch them individually. Combined with the full-spectrum-converted camera, it will be possible to obtain 12 instead of the usual 3 (red-green-blue) image layers.

Equipment

I use professional micro four thirds cameras from Olympus/OM-System. They are highly versatile and designed to tolerate field use under harsh conditions, including heavy rain and low and high ambient temperatures. The relatively small sensor is more than good enough for most use-cases except printing at huge sizes. As some other modern cameras they can be remotely controlled and triggered with computers, tablets or phones.

Digital cameras: two OM-1 (one unmodified and one full-spectrum-modified) and one EM-1 Mk II.
Lenses are listed by type. The lenses in mounts other than MFT are used together with adapters.
- Macro lenses (magnification range): MFT 30 mm f:3.5 Macro (, UV-A1?), MFT 60 mm f:2.8 Macro (), MFT 90 mm f:3.5 Macro (), Classic OM 50 mm f:3.5 Macro (, UV-A1?) and Classic OM 30 mm f:3.5 for (, UV-A1?).
- Telephoto lenses: MFT Sigma 60 mm f:2.8, MFT 40-150 mm f:2.8, MFT 300 mm f:4, MFT tele-converters and . Classic OM 100 mm f:2.8.
- Normal lenses: MFT 12-40 mm f:2.8, MFT 17 mm f:1.8, MFT Sigma 19 mm f:2.8 (UV-A1), MFT 25 mm f:1.2, MFT Sigma f:1.4, MFT Sigma 30 mm f:2.8 (UV-A1), MFT 45 mm f:1.8. Nikkor AI 24 mm f:2.8 (UV-A1). OM Classic 28 mm, f:3.5, OM Classic 35 mm f:2.8. SOligor 35 mm f:3.5 (UV-A1).
- Wide lenses: MFT 8-25 mm f:4.
- Pinhole lenses: Thingyfy Pinhole Pro MFT (normal) and Thingyfy Pinhole S MFT (wide angle).
- Lens adapters: Adapters for using old and special lenses of other brands with MFT cameras, including one with a filter drawer and one “speed booster” focal length reducer. - Macro extension tubes, automatic for MFT, and manual for OM and M42. Focusing helicoids for macro photography with adapted lenses.
Lens filters are listed by type.
- UV- and IR-cut “band-pass”:
- Short pass: absorptive filter stacks and interference filters in two different diameters. Suitable for UV-A photography in sunlight and electronic flash illumination.
- Long-pass: Multiple filters with cut-off wavelengths from 360 nm to 940 nm. As many absorptive glass filters fluoresce these filters can be combined to with interference and other non-fluorescent filters.
Illumination:
- Flash: Olympus FL-36 (VIS), Godox AD200 with interchangeable heads. One head custom modified to attach glass filters to constrain the range of wavelengths to UV, VIS or NIR (UV-B, UV-A, VIS, NIR). Battery operated and suitable for field use.
- Commercial LED lamps: Special portable small LED panels with very high colour reproduction index (CRI) specification, with adjustable colour temperature and dimming. Dimming NIR “video” lights. Flashlights emitting pure UV-A, Blue and NIR radiation suitable for field use. LED ring lamp for macro photography.
- Custom LED sources and drivers: I have a large collection of high power LEDs and the equipment to drive them. These include very high CRI white light high-power LEDs, multichannel LED arrays and medium power LEDs with peaks of emission at many different wavelengths between 280 nm and 1000 nm.
Camera, flash and LED control:
- Tethering: OM Capture (computer, USB, Wifi), OI.Share (Phone, Bluetooth, Wifi).
- Triggers: wireless and wired camera and flash triggers. In addition to cameras’ built-in modes for timed and time lapse photography, separate timers and triggers responsive to IR beam interruption and sound. Custom made triggers for triggering cameras and flashes from computers, using Python, R or other programing languages (useful for synchronizing image acquisition with illumination or data acquisition with computer controlable instruments such as spectrometers).
- Custom-assembled computer-controlled LED driver with 16 channels can also trigger cameras or instruments using a Python script or program in a computer.
Supports: I have standardised all support systems I use for photography on the use of Arca compatible rails, plates, clamps, etc.
- Travel and medium weight carbon fibre tripods with articulated central column. “Platypod” style tripods. Ball heads and Z-heads.
- Copy stand for macro-photography and for digitizing film.
- Different types of clamps and “magic arms”.
- Valoi 360 film holders for film sizes 120, 135, 127 and 110, plus 35 mm slide holder.
Software:
- RAW file conversion and editing: Capture One Pro, RawDigger, OM Workspace.
- Multi-image merging: Helicon Focus, Capture One Pro, OM Workspace, cameras.
- Colour profile generation: Lumariver Profile Designer.

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Data Analysis and Visualization

Pedro J. Aphalo "Photo Spectrum Services" — Fri, 05 Jun 2026 21:00:00 GMT

Experience

Although in the past I have also used other software, for several years now I have mainly used R together with package ‘ggplot2’ and its extensions. I have published and maintain several of these extension packages as well as contributed code and enhancement ideas to both ‘ggrepel’ and ‘ggplot2’.

I have taught R and data analysis and statistics both at the University of Jyväskylä and at the University of Helsinki, and as thesis supervisor or advisor and as collaborator adviced doctoral students, postdocs and principal investigators from multiple countries. As a collaborator in other researchers as well as within my own research group I have designed or advised on the design of many different experiments in the plant and ecological sciences, including forestry, agriculture, horticulture and basic plant research.

In 2002 I designed and taught one of the first R courses in Finland included in an M.Sc. level curriculum. I am the author of the book Learn R: As a Language published in The R Series now in its second edition, aimed at users of R in applied fields. I am also the lead editor and a co-author of the handbook on research methods Beyond the Visible: A handbook of best practice in plant UV photobiology.

Years of experience during which I strived to remain up-to-date with new data analysis and visualization methods have given me a broad experience and viewpoint from which to assess the advantages and disadvantages of different designs applicable to various research problems. Being familiar with practical issues, statistical design and data analysis methods, and with the design of effective visualizations for communicating the outcomes, provides me with an integrated perspective across all stages spanning from conceptualization of a study to the communication of results.

Computer Programming

I am proficient in R programming and I can write highly performant code within the R language. I have also experience in calling Python, Java and C++ routines from R code and in R packages. I have also written large programs and libraries in Modula 2. I have experience with other languages, including C++, Pascal, AWK and Perl. I can read Python, Forth, C, FORTRAN and Java code.

I am familiar with and apply software engineering principles conducive to maintainable and reliable software design and coding, including the use of unit tests in R packages, revision control with Git, and thorough documentation. I regularly use code debugging, benchmarking and profiling tools. I strive and regularly succeed in designing software that is user friendly.

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