Optical sensing and imaging

Spectral imaging
Keywords: spectral imaging; color; sensing applications for medicine, forestry, environment, and biology;

Computational spectral imaging

The group is a joint research group of the School of Computing and the Department of Physics and Mathematics. It belongs to the Institute of Photonics. Group is also member of the Academy of Finland’s Flagship on Photonics Research and Innovation (PREIN).

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Spectromics laboratory

Spectromics Laboratory is the first spectral imaging research environment in Finland focused in plant imaging.

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Environmental and medical photonics
Keywords: biophotonics; biomedical imaging; neurophotonics; Raman spectroscopy; Surface-Enhanced Raman Spectroscopy (SERS) ; black silicon; surface-enhanced Raman spectroscopy; gold nanoparticles; graphene; biocompatibility; enhancement factor; small organic molecules; living cells; nanodiamonds; color center; carbon nanotube; graphene quantum dot; theranostic agent

Surface-enhanced Raman spectroscopy (SERS)

The group is currently focused on the design, modeling and fabrication of a range of surface-enhanced Raman spectroscopy substrates based on black silicon (bSi). We propose to sculpture the bSi surface enhanced with graphene and / or gold nanolayers in order to achieve SERS enhancement factor as high as 8 orders of magnitude. This finding makes the SERS-active bSi-based substrate suitable for a number of the environmental and / or biomedical applications when detecting analytes’ trace concentrations are required. Being biocompatible, the bSi/Au SERS-active substrate offers a unique opportunity to monitor the functional state of living cells using  proteins / lipids / DNA/ RNA  characteristic Raman bands as markers.

Highly uniform and reliable bSi based SERS substrates provide a pathway to the  sensitive and selective, scalable, and low-cost lab-on-a-chip SERS biosensors that can be integrated into silicon-based photonics device.

In research, the group actively collaborates with international partners from Center for Physical Sciences and Technology, Vilnius, Lithuania. 

Contact persons:
Prof. Yuri Svirko
Prof. Polina Kuzhir
Dr. Petri Karvinen
PhD student Marina Fetisova
PhD student Hamza Rehman 

Selected publications:

  1. L. Golubewa, R. Karpicz, I. Matulaitiene, A. Selskis, D. Rutkauskas, A. Pushkarchuk, T. Khlopina, D. Michels, D. Lyakhov, T. Kulahava, A. Shah, Y. Svirko, and P. Kuzhir, “Surface-enhanced Raman spectroscopy of organic molecules and living cells with gold-plated black silicon”, ACS Appl. Mater. Interfaces 12, 50971 (2020).
  2. L. Golubewa, H. Rehman, T. Kulahava, R. Karpicz, M. Baah, T. Kaplas, A. Shah, S. Malykhin, A. Obraztsov, D. Rutkauskas, M. Jankunec, I. Matulaitiene, A. Selskis, A. Denisov, Y. Svirko, and P. Kuzhir, “Macro-, micro- and nano-roughness of carbon-based interface with the brain cells: towards a versatile bio-sensing platform”, Sensors 20, 5028 (2020).

Black silicon, surface-enhanced Raman spectroscopy, gold nanoparticles, graphene, biocompatibility, enhancement factor, small organic molecules, living cells 

Comparison of Raman spectra of 4-MBA monolayer on SiO2/Au smooth substrate (a), of bulk 4-MBA (b), and SERS spectra of 4-MBA (c) and living rat glioma cell (d) on the bSi/Au substrate. The spectrum of a living cell was recorded in aqueous Hepes-buffer solution. Buffer spectrum was subtracted from living cells Raman spectra. The excitation wavelength is 785 nm.

Uniformity of bSi/Au SERS substrate. (a) – Top-down SEM image of bSi/Au substrate, inset gives 1×1 μm area. (b) – Map of the background-corrected Raman intensity. 1077 cm-1 C–S stretch vibration peak, a 50× objective (NA 1.0) were used. The map resolution is 1 μm. 1,2,3 – separate 10×10 μm maps taken randomly from a 75×115 μm area. Inset gives a SERS spectrum of 4-MBA monolayer from 1×1 μm pixel.

Medical photonics

Group currently performs theoretical modeling and experimental verification of using photonic materials of reduced dimensionality for combining medical diagnosing and treatment in vitro. This approach is often dubbed “theranostics”. 

Single wall carbon nanotubes were proved to be effective theranostic agent, suitable for both detection of the cancer cells and their treatment non-invasive for surrounded healthy cells though cold photoacoustic mechanism. 

Our ambition is to create and validate in vitro a simple, robust and scalable multimodal quantum theranostic agents - fluorescent nanodiamonds and single-crystalline diamond needles embedding color centers, and graphene and other 2D materials-based quantum dots - capable of monitoring the functional state of electrically active cells, i.e. neurons, and destroying cancer cells.  

In research, the group actively collaborates with international partners from Center for Physical Sciences and Technology, Vilnius, Lithuania; Ulm University/ Institute for Quantum Optics, Ulm, Germany; Tor Vergata University/Department of Physics, Rome, Italy; University of Warsaw/ Quantum Optics Lab, Warsaw, Poland; Institute of Physics, National Academy of Science, Mink, Belarus 

Contact persons:
Prof. Yuri Svirko
Prof. Polina Kuzhir
Prof. Alexander Obraztsov
Dr. Sergei Malykhin
PhD student Hamza Rehman 

Selected publications:
L. Golubewa, I. Timoshchenko, O. Romanov, R. Karpicz, T. Kulahava, D. Rutkauskas, M. Shuba, A. Dementjev, Y. Svirko, and P. Kuzhir, “Single-walled carbon nanotubes as a photo-thermo-acoustic cancer theranostic agent: theory and proof of the concept experiment”, Sci. Rep. 10, 22174 (2020).

Nanodiamonds, color center, carbon nanotube, graphene quantum dot, theranostic agent

Numerical simulation of the interaction of laser radiation with the SWCNT agglomerate embedded into the living cell. Contour maps of the a temperature increase and b negative pressure in the SWCNT agglomerate of 1 µm aggregated inside the glioma cell on the pulse duration/intensity plane. c Isotherms at ΔT = 20 K and ΔT = 60 K, respectively, and isobar at ΔP = – 0.7 MPa. The star corresponds to the experimental conditions. 

Photo-induced SWCNT-mediated destruction of glioma cells by NIR pico-second pulsed irradiation. a-c Bare C6 glioma cells; d-f C6 glioma cells with accumulated micron-sized SWCNT agglomerates, g-i C6 glioma cells in the presence of the SWCNTs suspension in the extracellular medium. a, d, g bright-field images superimposed with PI fluorescence images before irradiation; b, e, h CARS images; c, f, i bright-field images superimposed with PI fluorescence images after irradiation with 10 ps laser pulses (910.5/1064 nm, 106 W/cm2) for 7 min. 


Computational imaging and modelling

Keywords: Inverse problems; radiative transfer; light transport; ultrasound; photoacoustics; optical imaging; optical tomography; photoacoustic imaging; tomography; ultrasonics; ultrasound therapy; HIFU; schlieren

Computational imaging and modelling

The group is part of Computational Physics and Inverse Problems research at the Department of Applied Physics. It belongs to the Institute of Photonics. The group is also a member of the Academy of Finland’s Flagship on Photonics Research and Innovation (PREIN) and Centre of Excellence in Inverse Modelling and Imaging. Furthermore, it holds an ERC Consolidator grant.

The research topics of the group include computational inverse problems and modelling with special interests in quantitative imaging, Bayesian inverse problems and uncertainty quantification. Furthermore, the group has strong expertise on computational modelling of light and ultrasound propagation. The group is especially interested in development of light, ultrasound and coupled physics based imaging modalities and therapy.

We have a strong international collaboration network with partners, for example, in the University College London, Politecnico di Milano and Sunnybrook Research Institute in Toronto.


Biomedical Optical Imaging and Ultrasound Laboratory (OPUS) is located at the Department of Applied Physics, Kuopio campus. The laboratory is equipped to perform versatile and demanding ultrasonic measurements. The facilities can be used to tune and calibrate commercial and prototype-level transducers and to measure acoustic pressure fields. The laboratory premises and equipment are available for in vitro, ex vivo, and in vivo experiments. Furthermore, the laboratory has facilities for diffuse optical tomography and photoacoustic tomography experiments and research. These can be applied for different measurement scenarios and they can be applied with e.g. biological samples and phantom targets.

The laboratory includes, for example, the following devices:

  • Two motorized and one manual 3D position systems, μm scale movements. Motorized positioners are under computer control.
  • Calibrated hydrophones for MHz range ultrasonics
  • Transducer from 0.5 MHz up to approximately 12 MHz
  • Ultrasound pulser and receiver electronics
  • RF generators and amplifiers
  • Computer controlled radiation force balance with forwarded/reflected electric power measurement
  • Schlieren system for 0.8 to 80 MHz frequency bandwidth
  • Laser vibrometer for surface velocity and displacement measurements up to 10 MHz
  • Nd:YAG – OPO laser with fiber optic coupling. Optical energies up to several hundreds of millijoules, wavelength range from 660 to 2600 nm, pulse duration ≈ 5 ns.
  • Sensors and meters for optical energy measurement from nanojoules to joules
  • Optical detectors for pulse duration measurement from < 1 ns
  • High-definition oscilloscope with 2.5 GHz bandwidth
  • Commercial and in-house built drive circuits for LEDs and laser diodes

See the full list of devices here: https://sites.uef.fi/opus/

Open software

We have an open source optical Monte Carlo code and MATLAB toolbox ValoMC for simulating light transport in scattering medium.

Group members

List of publications

See the list of publications here: https://sites.uef.fi/inverse/publications/


Other optical measurements

SIB Labs

The colour research laboratory is equipped with modern high-quality spectrometry and spectral imaging devices.

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Sm4rtlab is totally new, revolutionary augmented reality environment combining science and teaching.

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