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PROJECTS

BIOMEDICAL IMAGE ANALYSIS
AND MICRO-BIO ROBOTICS

MICRO-ROBOTICS

Micro-robotics represents a synthesis of physics, robotics and image analysis. Our research and experimental work is oriented to their application in biophysics. We exploit two-photon polymerization apparatus to fabricate micro-machines parts and holographic optical tweezers to manipulate with them.

Viscosity measurement

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Bending of a flexible cantilever structure by optical tweezers. After switching the trapping laser off, the cantilevers moved back to the initial equilibrium in an overdamped oscillatory regime. The video analysis of the recovery motion was used to determine the cantilever’s visco-elastic characteristics (see Kubackova 2020). For viscosity measurement, the deflection angle only about 10 degrees is used.
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Micro-manipulation

Fork

Holographic Optical Tweezers (HOT) creates several independently movable laser traps that are able to move transparent particles. Using a special interface, the position of traps can be controlled by fingers.
Direct manipulation could damage live cells and therefore their indirect manipulation through a proper tool is preferred. One such tool is fork-like microstructure prepared by two photon polymerization (2PP).
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Path planning

Fork

Path planning is a strategy how to move a particle to the destination without the collision with an obstacles. This strategy is important for any autonomous robot.
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SOFTWARE

This section contains programs for image analysis and cells counting in 2D and 3D. All programs are free for download. Their input is either single image (NeuroCounter) two sections (DisectCounter) or a series of optical sections obtained from a confocal microscope (ConfoCounter).

DisectCounter

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Estimation of the total number of objects in 3D volume by "Disector" method.
Method counts objects terminating between two (properly sampled and aligned) 2D sections.
Counting is performed on selected Stereological counting frames used for the total count estimation.
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NeuroCounter

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Image analysis program for semi=interactive particles detection and quantification.
Program detects particles and calculates corresponding features (like area, diameter, circularity) inside the stereological counting frames.
The estimated values valid for the whole image are calculated and saved in a text format readable by Excel.
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ConfoCounter

Microsoft Azure

Estimates the number of cells inside the volume of interest using 3D stereological probe.
Extended version supplied with eye tracker helps to find the last cell's section in Z-stack by gaze
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SELECTED PAPERS

(Click HERE to show full list and PDFs from ResearchGate)

  • T. Tadokoro, M. Bravo-Hernandez, K. Agashkov, Y. Kobayashi, O. Platoshyn, M. Navarro, S. Marsala, A. Miyanohara, T. Yoshizumi, M. Shigyo, V. Krotov, S. Juhas, J. Juhasova, D. Nguyen, H. Kupcova Skalnikova, J. Motlik, H. Studenovska, V. Proks, R. Reddy, S. P. Driscoll, T. D. Glenn, T. Kemthong, S. Malaivijitnond, Z. Tomori, I. Vanicky, M. Kakinohana, S. L. Pfaff, J. Ciacci, P. Belan, and M. Marsala, “Precision spinal gene delivery-induced functional switch in nociceptive neurons reverses neuropathic pain,” Molecular Therapy, vol. 30, no. 8, pp. 2722-2745, 2022.
  • J. Kubacková, C. Slabý, D. Horvath, A. Hovan, G. T. Iványi, G. Vizsnyiczai, L. Kelemen, G. Žoldák, Z. Tomori, and G. Bánó, “Assessing the viscoelasticity of photopolymer nanowires using a three-parameter solid model for bending recovery motion,” Nanomaterials, vol. 11, no. 11, 2021.
  • G. Bánó, J. Kubacková, A. Hovan, A. Strejčková, G. T. Iványi, G. Vizsnyiczai, L. Kelemen, G. Žoldák, Z. Tomori, and D. Horvath “Power Spectral Density Analysis of Nanowire-Anchored Fluctuating Microbead Reveals a Double Lorentzian Distribution,” Mathematics, vol. 9, no. 15, pp. 1748, 2021.
  • Z. Dzurjaskova, J. Blasko, Z. Tomori, and I. Vanicky “A method to prepare large resin sections for counting myelinated axons in rodent CNS and PNS structures,” Neuroscience Letters, vol. 750, Apr, 2021.
  • J. Kubackova, G. T. Ivanyi, V. Kazikova, A. Strejckova, A. Hovan, G. Zoldak, G. Vizsnyiczai, L. Kelemen, Z. Tomori, and G. Bano. "Bending dynamics of viscoelastic photopolymer nanowires." Appl. Phys. Lett. vol. 117, 013701, 2020.
  • M. Bravo-Hernandez, T. Tadokoro, M. R. Navarro, O. Platoshyn, ... Z. Tomori, ..., D.D. W. Cleveland, M. Marsala, "Spinal subpial delivery of AAV9 enables widespread gene silencing and blocks motoneuron degeneration in ALS," Nature Medicine, vol. 26, pp. 118-130, 2020. ( PDF)
  • Z. Tomori, V. Kazikova, J. Kubackova, and G. Bano, "Video analysis of polymerized micro-cantilever deflected by the laser trap," Proc. SPIE, Optical Trapping and Optical Micromanipulation vol. 11083, K. Dholakia and G. C. Spalding, Eds., 2019.
  • M. Korabecna, Z. Tonar, Z. Tomori, E. Demjen. Optimized cutting laser trajectory for laser capture microdissection, Biologia vol. 74, pp. 717-724, 2019
  • A. Matiasova, J. Sevc, Z. Tomori, Z. Gombalova, S. Gedrova, and Z. Daxnerova, "Quantitative Analyses of Cellularity and Proliferative Activity Reveals the Dynamics of the Central Canal Lining During Postnatal Development of the Rat," Journal of Comparative Neurology, vol. 525, pp. 693-707, Feb 2017.
  • Z. Tomori, P. Kesa, M. Nikorovic, J. Kanka, P. Jakl, M. Sery, S. Bernatova, E. Valusova, M. Antalik, and P. Zemanek, “Holographic Raman tweezers controlled by multi-modal natural user interface,” Journal of Optics, vol. 18, no. 1, pp. 015602, 2016.
  • L. Dancakova, T. Vasilenko, I. Kovac, K. Jakubcova, M. Holly, V. Revajova, F.k Sabol, Z. Tomori, M. Iversen, P. Gal, J. M. Bjordal ."Low-Level Laser Therapy with 810 nm Wavelength Improves Skin Wound Healing in Rats with Streptozotocin-Induced Diabetes." Photomedicine and laser surgery 32 (3) 2014 pp. 198-205;
  • Z. Tomori, M. Antalik, P. Kesa, J. Kanka, P. Jakl, M. Sery, S. Bernatova, P. Zemanek. "Holographic Raman Tweezers Controlled by Hand Gestures and Voice Commands" Optics and Photonics Journal 3(2B):331-336.
  • R. Navarro, S. Juhas, S. Keshavarzi, J. Juhasova, J. Motlik, K. Johe, S. Marsala, M. Scadeng, P. Lazar, Z. Tomori, G. Schulteis, M. Beattie, J. D.Ciacci, and M. Marsala, "Chronic Spinal Compression Model in Minipigs: A Systematic Behavioral, Qualitative and Quantitative Neuropathological Study" Journal of Neurotrauma, vol. 29, pp. 499-513, Feb 2012.
  • H. Gojzewski, M. Makowski, A. Hashim, P. Kopcansky, Z. Tomori, and M. Timko, "Magnetosomes on Surface: An Imaging Study Approach", SCANNING, vol. 33, pp. 1-10, 2011.
  • E. Demjen, V. Abosi, and Z. Tomori, "Eye tracking using artificial neural networks for human computer interaction", Physiological research , vol. 60, pp. 841-4, 2011-Nov-22 2011.

PROJECTS

Projects of Slovak Research and Development Agency (APVV) - principal investigator

  • Image analysis of microscopic particles in the automation of optical manipulation techniques applicable in micro/nanorobotics (2016-2020).
  • Interactive methods of image acquisition and processing in microscopy using natural user interface (2012-2015).
  • Fluorescent image analysis of irregularly shaped cells for purposes of non-destructive DNA contents quantification (2008-2010).

Projects of Slovak Scientific Grant Agency (VEGA) - principal investigator

  • Natural User Interface based on RGB-D Image Processing Algorithms and their Application in Biomedicine. (2016-2018)
  • Interactive image processing algorithms based on energy minimization and "Graph-cuts" method (2011-2013).
  • The methods of images sequence segmentation using active contours and their exploitation in biomedicine (2008-2010).
  • Interactive algorithms of segmentation based on the active contours model and their application in the measurement of physical parameters of biomedical objects (2005-2007).
  • Fast hierarchical segmentation of biomedical images and its using in medical diagnostics (2001-2003).

International projects of bilateral cooperation - principal investigator

  • Elastic micro-tools for optical manipulation of biological objects. Slovak-Hungarian bilateral project (2019 - 2022).
  • Processing and analysis of three-dimensional biomedical images. Slovak-Czech bilateral project (2010-2011).
  • Recognition, visualization and measurement of fiber-like structures in 3D space. Slovak-Czech bilateral project (2008-2009).
  • Measurement of geometrical characteristics of fiber-like structures in 2D and 3D by using of active contours models.Slovak-Czech bilateral project (2004-2005).
  • Integrated system of program modules for the analysis of biomedical images in 3D. Slovak-Czech bilateral project (2002-2003).
  • Development of software tools (modules) for the estimation and analysis of image data representing biomedical volume. Slovak-Czech bilateral project (2000-2001).

CONTACT

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Zoltan Tomori, PhD, Assoc Prof
Institute of Experimental Physics,
Slovak Academy of Sciences

Watsonova 47, 04001 Kosice, Slovakia
Phone: +421 55 7922340
Email: tomori@saske.sk

Staff:

Jana Kubackova, PhD
Email: kubackova@saske.sk
Part time: Ing. Igor Hrmo

External: Gregor Bano, PhD., Assoc. Prof
Cooperations: see list of publications.