Härkönen, T., Wade, S., Law, K.,  Roininen, L. (2022). Mixtures of Gaussian Process Experts with SMC2arXiv, 2208.12830.

Saghi, A., Junjuri, R., Lensu, L., & Vartiainen, E. M. (2022). Semi-synthetic data generation to fine-tune a convolutional neural network for retrieving Raman signals from CARS spectra. Optics Continuum, accepted.

Junjuri, R., Saghi, A., Lensu, L., & Vartiainen, E. M. (2022). Effect of non-resonant background on the extraction
of Raman signals from CARS spectra using deep neural networks. RCA Advances, accepted.

Härkönen, T., Hannula, E. Moores, M. T., Vartiainen, E. M., & Roininen, L. (2022). A Log-Gaussian Cox Process with Sequential Monte Carlo for Line Narrowing in Spectroscopy. arXiv, 2202.13120.

Junjuri, R., Saghi, A., Lensu, L., & Vartiainen, E. M. (2022). Convolutional neural network-based retrieval of Raman signals from CARS spectra. Optics Continuum 1, 1324-1339.

 Hulkko, E., Pikker, S., Tiainen, V., Tichauer, R. H., Groenhof, G., & Toppari, J. J. (2021). Effect of molecular Stokes shift on polariton dynamics. The Journal of Chemical Physics154(15), 154303.

Kurttila, M., Stucki-Buchli, B., Rumfeldt, J., Schroeder, L., Häkkänen, H., Liukkonen, A., Takala, H., Kottke, T. & Ihalainen, J. (2020). Site-by-site tracking of signal transduction in an azidophenyalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy. Physical Chemistry Chemical Physics, 23(9), 5615-5628.

 Härkönen, T., Roininen, L., Moores, M. T., & Vartiainen, E. M. (2020). Bayesian Quantification for Coherent Anti-Stokes Raman Scattering Spectroscopy. Journal of Physical Chemistry B124(32), 7005-7012.

Related publications

Nonlinear optical imaging

 Ojarinta, R., Saarinen, J., Strachan, C. J., Korhonen, O., & Laitinen, R. (2018). Preparation and characterization of multi-component tablets containing co-amorphous salts: Combining multimodal non-linear optical imaging with established analytical methods.European Journal of Pharmaceutics and Biopharmaceutics, 132(September), 112–126.

Saarinen, J., Gütter, F., Lindman, M., Agopov, M., Fraser-Miller, S. J., Scherließ, R., … Strachan, C. J. (2018). Cell-Nanoparticle Interactions at (Sub)-Nanometer Resolution Analyzed by Electron Microscopy and Correlative Coherent Anti-Stokes Raman Scattering. Biotechnology Journal, 8, 1–10.

Saarinen, J., Sözeri, E., Fraser-Miller, S. J., Peltonen, L., Santos, H. A., Isomäki, A., & Strachan, C. J. (2017). Insights into Caco-2 cell culture structure using coherent anti-Stokes Raman scattering (CARS) microscopy. International Journal of Pharmaceutics, 523(1), 270–280.

Novakovic, D., Saarinen, J. K. S., Rojalin, T. P., Antikainen, O., Fraser-Miller, S. J., Laaksonen, T., … Strachan, C. J. (2017). Multimodal Non-linear Optical Imaging for Sensitive Detection of Multiple Pharmaceutical Solid-State Forms and Surface Transformations. Analytical Chemistry, 89, 11460-11467.

Darville, N., Saarinen, J., Isomäki, A., Khriachtchev, L., Cleeren, D., Sterkens, P., … Van den Mooter, G. (2015). Multimodal non-linear optical imaging for the investigation of drug nano-/microcrystal-cell interactions. European Journal of Pharmaceutics and Biopharmaceutics Journal, 96, 338–348.

Christophersen, P. C., Birch, D., Saarinen, J., Isomäki, A., Nielsen, H. M., Yang, M., … Mu, H. (2014). Investigation of protein distribution in solid lipid particles and its impact on protein release using coherent anti-Stokes Raman scattering microscopy. Journal of Controlled Release, 197, 111-120.

Laser modification of 2D material properties:

Hiltunen, V. M., Koskinen, P., Mentel, K. K., Manninen, J., Myllyperkiö, P., Johansson, A., & Pettersson, M. (2020). Making Graphene Luminescent by Direct Laser Writing. The Journal of Physical Chemistry C124(15), 8371-8377.

Koskinen, P., Karppinen, K., Myllyperkiö, P., Hiltunen, V. M., Johansson, A., & Pettersson, M. (2018). Optically Forged Diffraction-Unlimited Ripples in Graphene. The Journal of Physical Chemistry Letters9(21), 6179-6184.

Johansson, A., Myllyperkiö, P., Koskinen, P., Aumanen, J., Koivistoinen, J., Tsai, H. C., … & Woon, W. Y. (2017). Optical forging of graphene into three-dimensional shapes. Nano Letters17(10), 6469-6474.

Aumanen, J., Johansson, A., Koivistoinen, J., Myllyperkiö, P., & Pettersson, M. (2015). Patterning and tuning of electrical and optical properties of graphene by laser induced two-photon oxidation. Nanoscale7(7), 2851-2855.

Coherent spectroscopy and imaging:

Koivistoinen, J., Myllyperkio, P., & Pettersson, M. (2017). Time-resolved coherent anti-Stokes Raman scattering of graphene: dephasing dynamics of optical phonon. The Journal of Physical Chemistry Letters8(17), 4108-4112.

Koivistoinen, J., Aumanen, J., Hiltunen, V. M., Myllyperkiö, P., Johansson, A., & Pettersson, M. (2016). Real-time monitoring of graphene patterning with wide-field four-wave mixing microscopy. Applied Physics Letters108(15), 153112.

Aumanen, J., Johansson, A., Herranen, O., Myllyperkiö, P., & Pettersson, M. (2015). Local photo-oxidation of individual single walled carbon nanotubes probed by femtosecond four wave mixing imaging. Physical Chemistry Chemical Physics17(1), 209-216.

Kotiaho, A., Myllyperkiö, P., & Pettersson, M. (2014). Chemically selective imaging of overlapping C–H stretching vibrations with time-resolved coherent anti-stokes Raman scattering (CARS) microscopy. The Journal of Physical Chemistry B118(16), 4363-4369.

Myllyperkio, P., Herranen, O., Rintala, J., Jiang, H., Mudimela, P. R., Zhu, Z., … & Pettersson, M. (2010). Femtosecond four-wave-mixing spectroscopy of suspended individual semiconducting single-walled carbon nanotubes. ACS Nano4(11), 6780-6786.

Quantitative coherent Raman spectroscopy and imaging

 Bureš, J., Eerola, T., Lensu, L., Kälviäinen, H., Zemčík, P., 2021. Plankton Recognition in Images with Varying Size, Pattern Recognition. ICPR International Workshops and Challenges, Lecture Notes in Computer Science. Springer International Publishing, Cham, pp. 110–120.

Dutta, A. & Vartiainen, E. M. (2020). Spatial localization of hotspots in Fano-resonant plasmonic oligomers for surface-enhanced coherent anti-Stokes Raman scattering. Journal of European Optical Society – Rapid Publications16(8).

A. Garifullin, P. Kööbi, P. Ylitepsa, K. Ådjers, M. Hauta-Kasari, H. Uusitalo, L. Lensu, 2018. Hyperspectral Image Segmentation of Retinal Vasculature, Optic Disc and Macula, in: 2018 Digital Image Computing: Techniques and Applications (DICTA), pp. 1–5.

Bartczak, P., Fält, P., Penttinen, N., Ylitepsa, P., Laaksonen, L., Lensu, L., Hauta-Kasari, M., Uusitalo, H., 2017. Spectrally optimal illuminations for diabetic retinopathy detection in retinal imaging. Optical Review 24, 1–12.

Laaksonen, L., Claridge, E., Fält, P., Markku Hauta-Kasari, Uusitalo, H., Lensu, L., 2017. Comparison of image registration methods for composing spectral retinal images. Biomedical Signal Processing and Control 36, 234–245.

Kan, Y., Lensu, L., Hehl, G., Volkmer, A., & Vartiainen, E. M. (2016). Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses. Optics Express24(11), 11905-11916.

Nguyen, U., Laaksonen, L., Uusitalo, H., Lensu, L., 2016. Reconstruction of retinal spectra from RGB data using a RBF network, in: The Sixth International Conference on Image Processing Theory, Tools and Applications, IPTA 2016. Oulu, Finland, 12-15 December 2016, pp. 1–6.

Vartiainen, E. M. & Peiponen, K.-E. (2013). Optical and terahertz spectra analysis by the maximum entropy method. Reports on Progress in Physics76(6), 066401.

Cicerone, M. T., Aamer, K. A., Lee, Y. J., & Vartiainen, E. M. (2012). Maximum entropy and time-domain Kramers–Kronig phase retrieval approaches are functionally equivalent for CARS microspectroscopy. Journal of Raman Spectroscopy43(5), 637-643.

Day, J. P. R., Domke, K. F., Rago, G., Hamaguchi, H., Vartiainen, E. M. & Bonn, M. (2011). Quantitative Coherent Anti-Stokes Raman Scattering (CARS) Microscopy. Journal of Physical Chemistry B115(24), 7713–7725.

Rinia, H. A., Bonn, M., Müller, M., & Vartiainen, E. M. (2007). Quantitative CARS Spectroscopy Using the Maximum Entropy Method: The Main Lipid Phase Transition. ChemPhysChem8(2), 279-287.

Vartiainen, E. M., Rinia, H. A., Müller, M., & Bonn, M. (2006). Direct extraction of Raman line-shapes from congested CARS spectra. Optics Express14(8), 3622-3630.

Vartiainen, E. M., Peiponen, K.-E., & Asakura, T. (1993). Generalized noniterative maximum entropy procedure for phase retrieval problems in optical spectroscopy. Optics Communications104(1-3), 149-156.

Vartiainen, E. M. (1992). Phase retrieval approach for coherent anti-Stokes Raman scattering spectrum analysis. Journal of the Optical Society of America B9(8), 1209-1214.