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| Elastic micro-tools for optical manipulation of biological objects | |
| Elastic micro-tools for optical manipulation of biological objects | |
| Program: | Inter-academic agreement |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Duration: | 1.1.2019 – 31.12.2022 |
National
| MikroFlex – Pružné mikroštruktúry a mikroroboty pre biomedicínske labon-chip aplikácie | |
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| Program: | SRDA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Annotation: | The development boom of biomedical lab-on-chip (LOC) applications during the last two decades brought the need for the miniaturization of conventional mechanical actuators, sensors, and manipulators. Light-driven mechanical microstructures, trapped and moved by optical tweezers, can be easily integrated into the microfluidic LOC environment. The vast majority of light-driven microstructures is prepared by two-photon polymerization. It is the main objective of the present project to exploit the possibilities of working with flexible (deformable) microstructures, which were not used in biomedical applications, yet. Two well-defined LOC application areas are targeted: micro-rheology and single-cell manipulation. Micro-viscometers utilizing the effect of the surrounding fluid medium on the deformation (deflection) of flexible micro-cantilevers will be developed. The novel viscometer devices will be either anchored to the bottom glass surface or kept mobile and optically transportable inside the micro-fluidic system. Light-driven elastic micro-robots will be designed and tested for capture, transport, and release of single live cells. The operation of the developed micro-manipulators will be automated to build multicellular systems, mimicking the tissue conditions, in an autonomous way. To facilitate the flexible microstructure development and optimization, the material properties of the photo-polymers will be determined by comparing experimental deformation data with the results of numerical simulations. |
| Duration: | 1.7.2022 – 30.6.2026 |
| Analýza obrazových sekvencií metódami hlbokého učenia vo vybraných biofyzikálnych experimentoch | |
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| Program: | VEGA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Duration: | 1.1.2022 – 31.12.2024 |
| Nový pohľad na vplyv hydrofóbnych interakcií na tvorbu a stabilitu proteínových agregátov. Prepojenie na oxidačný stres. | |
| New Insight into the Role of Hydrophobic Interactions in Formation and Stability of Proteins Aggregates. Link to Oxidative Stress. | |
| Program: | VEGA |
| Project leader: | MUDr. Musatov Andrey, DrSc. |
| Duration: | 1.1.2021 – 31.12.2023 |
| MICROMANIP – Obrazová analýza mikroskopických častíc pri automatizácii optických manipulačných techník aplikovateľných v mikro/nanorobotike. | |
| Image analysis of microscopic particles in the automation of optical manipulation techniques applicable in mikro/nanorobotics. | |
| Program: | SRDA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Annotation: | Mikromanipulation based on the laser optical traps represents a progressive method of basic research in the physical, chemical and biomedical sciences. An analogy between the optical manipulation and the robotics evokes exploitation of the artificial intelligence algorithms (computer vision, machine learning, planning of trajectories, etc.). According to some authors, the use of these methods in combination with physical models has led to the significant increase of the effectiveness compared to the classic optimization (up to 1000 times in SVM classifier trained in advance using the Lorenz-Mie scattering light model). The aim of the project is to use a similar philosophy for the experimental tasks solved in our laboratory – cells sorting and fusing, their physical properties measurement and etc. Using the apparatus for 2-photon polymerization we plan to manufacture microrobotic instruments controlled by the optical tweezers traps, e.g. a mikrorobotic arm (gripper). As continuity with our previous project, we would improve the interactive control of optical tweezers via NUI interface (using the position of the fingers and gaze, voice, gestures). This interface should be functional not only locally, but also remotely over a network connection. |
| Duration: | 1.7.2016 – 30.6.2020 |
| RGBD_Algorithms – Prirodzené užívateľské rozhranie na báze algoritmov spracovania RGB-D obrazu s využitím v biomedicíne | |
| Natural User Interface based on RGB-D Image Processing Algorithms and their Application in Biomedicine | |
| Program: | VEGA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Annotation: | New types of 3D sensors are designed to capture the human body or its parts. Their output is usually RGB color image, depth map, as well as 3D coordinates representing the position of the hands, fingers, and the gaze direction. One of the objectives of the project is to improve the manipulation with microscopic particles by using optical tweezers so that the position of the laser traps are controlled by the position of the fingers acquired by the Leap Motion sensor. The second goal is to exploit 3D sensors to support the rehabilitation training in both the clinic environment and at home (telerehabilitation). Contactless system will warn the patient for deviations from the rehabilitation protocol, the output of the program is an evaluation score proposed in close cooperation of programmers with physiotherapists. In doing so, they used the principles of machine learning, computer games, data transmission over the network classifiers and the other techniques in the field of computer vision and graphics. |
| Duration: | 1.1.2016 – 31.12.2018 |
| Štúdium stability a agregácie natívne rozbalených proteínov | |
| Study of the intrinsically disordered protein stability and aggregation | |
| Program: | VEGA |
| Project leader: | RNDr. Fedunová Diana, PhD. |
| Annotation: | Intrinsically disordered proteins (IDPs) – proteins without ordered stable structure at physiological conditions – are of great interest especially due to their connections to neurodegenerative diseases. Alzheimer’s disease is characterized by deposits of amyloid plaques or neurofibrillary tangles, formed by fibrous assemblies of the A-beta or tau proteins. The growing evidences indicate that oligomers are more toxic species than fibrils. Proposed projects is oriented on study of the effect of external conditions (pH, T, ionic strength, hydrophobicity) and various compounds (denaturants, osmolytes and polyanions) on conformation of tau and A-beta proteins andkinetics of their oligomerization. Another goal is to define how properties of oligomers affect the kinetics of ibrillization and morphology of obtained amyloid fibrils. |
| Duration: | 1.1.2014 – 31.12.2017 |
| MICRO_NUI – Interaktívny zber a spracovanie obrazov v mikroskopii použitím prirodzeného užívateľského rozhrania | |
| Interactive methods of image acquisition and processing in microscopy using natural user interface | |
| Program: | SRDA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Annotation: | Communication with computers via the natural user interface (NUI) has growing importance in several areas. Our goal is the utilization of specific NUI devices, e.g. Microsoft Kinect, touch tablet and the brain potentials sensor to control the „state of the art" experimental devices such as optical tweezers and optical scalpel. The project is aimed to propose new and modify existing algorithms in the field of computer vision and image analysis, that allow not only recognition of microscopic particles, but also automatic or semi-automatic manipulation of them. The part of this process is appropriate visualization in mono or stereo mode that represents a feedback of interactive algorithms. |
| Duration: | 1.7.2012 – 31.12.2015 |
| Interaktívne algoritmy spracovania obrazu založené na minimalizácii energetickej funkcie a metóde "Graph-cuts". | |
| Interactive Image Processing Algorithms Based on Energy Minimization and "Graph-cuts" Method | |
| Program: | VEGA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Annotation: | The goal of the project is to extend interactive capabilities of Graph-cuts algorithm. Our aim is to supply user with a set of tools represented as cursors of various shapes that would be automatically adapted according to properties of underlying image. This method will be tested on segmentation of individual pictures as well on off-line analysis of video records of moving objects. The modified version of this algorithm should perform 3D reconstruction based on the series of images capturing an object under different angles of view using the planned prototype for Molecular Fluorescence Tomography. |
| Duration: | 1.1.2011 – 31.12.2013 |
| EDUFYCE – Edukačné fyzikálne centrum ÚEF SAV | |
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| Program: | Štrukturálne fondy EÚ Vzdelávanie |
| Project leader: | RNDr. Zentková Mária, CSc. |
| Project webpage: | edufyce.saske.sk |
| Duration: | 1.9.2010 – 30.8.2013 |
| NMTE – Nové materiály a technológie pre energetiku | |
| New materials and technologies for energetics | |
| Program: | EU Structural Funds Research & Development |
| Project leader: | Ing. Diko Pavel, DrSc., akademik US Slovenska |
| Annotation: | Aims o the project are:1. Technology of nanostructured bulk superconductors for energy storage2. Biological battery based on renewable biological products3. New trafo-steel modified by nanoparticles 4. Cooling and insulating medium based on magnetic fluid for high power transformers |
| Project webpage: | nmte.saske.sk |
| Duration: | 1.5.2010 – 30.4.2013 |
| Dobudovanie centra pre kooperatívne javy a fázové prechody v nanosystémoch s pespektívou využitia v nano- a biotechnológiách | |
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| Program: | EU Structural Funds Research & Development |
| Project leader: | doc. RNDr. Kopčanský Peter, CSc. |
| Duration: | 1.4.2010 – 31.3.2013 |
| NANOFLUID – Centrum excelentnosti SAV – Nanokvapaliny | |
| Centre excelence of SAS – Nanofluids | |
| Program: | Centrá excelentnosti SAV |
| Project leader: | doc. RNDr. Kopčanský Peter, CSc. |
| Annotation: | Centre of NANOFLUIDS is oriented to development of technology of nanoparticles, as are magnetic nanoparticles, coloid gold, nanotubes and their complex characterisation from with aspect to their magnetic and morphologic properties. The prepared nanoparticles will be funcionalised for applications in biomedicine, biotechnology and electrotechnical industry. In the case of biomedical applications the interaction of nanoparticles with biomacromolecules will be investigated, mostly with aspect of the nanohazard, drug targeting delivery, hyperthermia and treatment many human diseases as e.g. Alzheimer\’s diseases, etc. For technical applications the centre will investigate opportunity of application in LCD’s, sensors of magnetic field, as an insulated and cooling medium in high power transformers and converters, exploation multilayered nanotubes and fullerenes as electrodes in device that could converts sun energy into electricity. |
| Duration: | 1.2.2009 – 31.1.2013 |
| Vývoj tecnologických postupov magnetických kvapalín pre biomedecínske účely | |
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| Program: | EU Structural Funds Research & Development |
| Project leader: | doc. RNDr. Kopčanský Peter, CSc. |
| Duration: | 1.1.2010 – 30.6.2012 |
| Proc3D – Spracovanie a analýza trojrozmerných biomedicínských obrazov | |
| Processing and analysis of three-dimensional biomedical images | |
| Program: | SRDA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Duration: | 1.1.2010 – 31.12.2011 |
| Kooperatívne javy a fázové prechody v nanosystémoch s perspektívou využitia v nano- a biotechnológiách | |
| Centre of excelence: Cooperative phenomena and phase transitions in nanosystems with perspective applications in nano- and biotechnology | |
| Program: | EU Structural Funds Research & Development |
| Project leader: | doc. RNDr. Kopčanský Peter, CSc. |
| Duration: | 24.4.2009 – 31.3.2011 |
| Analýza fluorescenčného obrazu nepravidelných buniek s cieľom nedeštruktívnej kvantifikácie DNA | |
| Fluorescent image analysis of irregularly shaped cells for purposes of non-destructive DNA contents quantification | |
| Program: | SRDA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Annotation: | Current non-destructive methods of DNA contents measurement in living cells are based either on densitometric analysis of static fluorescent images or on the dynamic acquisition of signal when a cell flows under the detector of flow cytometer. Both methods failed in irregularly shaped cells like e.g. sperm cells.Proposed project is based on the combination of both approaches that means controlled rotation of an immobilized sperm cell in a transparent capillary and acquisition of emitted light by CCD camera. The series of images representing the sperm cell under different angles of view leads to the design of a 3D model which allows comparison of flatten objects acquired under different conditions which make DNA measurement more objective. Automation of the experiment is based on the analysis of many immobilized sperm cells localized in the capillary which allows exploitation of such apparatus in the assisted reproduction centers where they could replace expensive and not very precise flow cytometer. This is a way how to avoid the using of defected sperm causing a transfer of genetic diseases. |
| Duration: | 1.6.2008 – 31.12.2010 |
| Metódy segmentácie postupnosti obrazov pomocou aktívnych kontúr a ich využitie v biomedicíne | |
| Methods of images sequence segmentation using active contours and their exploitation in biomedicine | |
| Program: | VEGA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Annotation: | The project solves the problem of the segmentation of image sequences representing either serial opticalsections obtained by a confocal microscope or time sequences of images obtained by a video camera. The mainmethod in our approach in segmentation is the active contour model. Our own modification is based on the wireconductor model and is proposed in this project. The algorithms of the segmentation will be tested on thefollowing applications: 3D reconstruction of microvessels net in the brain, determination of the chromosomesnumber in a sperm based on its shape analysis and mobility monitoring of minipigs suffering from Huntingtondisease. All these applications have the direct link to existing projects solved at cooperating institutions |
| Duration: | 1.1.2008 – 31.12.2010 |
| FIBER3D – Rozpoznávane, vizualizácia a meranie vláknitých štruktúr v 3D priestore | |
| Recognition, visualization and measurement of fiber-like structures in 3D space | |
| Program: | Podpora MVTS z prostriedkov SAV |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Duration: | 1.2.2008 – 31.12.2009 |
| Interaktívne algoritmy segmentácie na báze aktívnych kontúr a ich uplatnenie pri meraní fyzikálnych vlastností biomedicínskych objektov | |
| Interactive algorithms of segmentation based on active contour models and their exploatation in the measurement of physical parameters of biomedical objects | |
| Program: | VEGA |
| Project leader: | doc. Ing. Tomori Zoltán, CSc. |
| Duration: | 1.1.2005 – 31.12.2007 |