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Elastic registration of biomedical images on CUDA-Supported graphics procesor units
Michálek, Jan; Čapek, Martin; Janáček, Jiří; Kubínová, Lucie
2010 - English
Elastic registration is a task of finding the matching of two images, using geometric and elastic transformations, so that objects in images have the same size, position and orientation. We apply elastic registration in the framework of volume reconstruction, where an object acquired from parallel physical sections is composed and mutual positions of the sections including deformations caused by their cutting have to be found. The method lies in optimizing a functional consisting of two parts: first, discrete total variation as a measure of roughness and, second, L1 norm as a measure of dissimilarity of images. As a parallelizable optimization strategy we apply a potential-based equivalent transformation of a (max,+)-labelling problem. CUDA-based implementation of the described elastic registration algorithm is reasonably fast, requires seconds to minutes of calculations, provides good results and, thus, can be used for practical tasks dealing with alignment of biomedical images
Keywords:
volume reconstruction; elastic alignment; CUDA
Available at various institutes of the ASCR
Elastic registration of biomedical images on CUDA-Supported graphics procesor units
Elastic registration is a task of finding the matching of two images, using geometric and elastic transformations, so that objects in images have the same size, position and orientation. We apply ...
Multi-photon excitation microscopy
Chernyavskiy, Oleksandr; Kubínová, Lucie
2008 - English
Multiphoton excitation microscopy (MPM), being some time ago rather exotic than an easy-to-handle tool, becomes now more widely used due to advances in laser technique. This promising, yet expensive technique provides such advantages, as deeper penetration depth, lower photodamage, especially important in live cells imaging for extended periods of time Multifotonová excitační mikroskopie se z exotické techniky postupně stává stále více používaným nástrojem díky pokroku v laserové technice. Tato slibná i když náročná technika poskytuje výhody, jako je průnik do větší hloubky, nižší fotopoškození, jež jsou zvláště užitečné při dlouhodobém zobrazování buněk
Keywords:
two-photon excitation; multiphoton excitation; second-harmonic generation
Available at various institutes of the ASCR
Multi-photon excitation microscopy
Multiphoton excitation microscopy (MPM), being some time ago rather exotic than an easy-to-handle tool, becomes now more widely used due to advances in laser technique. This promising, yet expensive ...
Effects of dietary polyunsaturated fatty acids on myocardial and serum lipids in normoxic and chronically hypoxic rat heart
Balková, P.; Ježková, J.; Hlaváčková, M.; Neckář, Jan; Staňková, B.; Kolář, František; Novák, F.; Nováková, O.
2008 - English
The goal of this study was to fellow up the effect of n-3 and n-6 polyunsaturated fatty acids (PUFA) and the adaptation to chronic intermittent hypoxic (CIH) on fatty acid (FA) composition of serum and heart lipids in rats. The results of this study showed that PUFA diets and CIH distinctly modified FA profile in serum and heart lipids; both interventions considered to be cardioprotective Cílem práce bylo sledovat změny srdečních a sérových lipidů potkana po dlouhodobé dietě obohacené o n-3 a n-6 polynenasycené mastné kyseliny (PUFA) a adaptaci na chronickou intermitentní hypoxii (CIH). Studie ukázala, že jak dieta obohacená o PUFA tak CIH zásadně modifikují složení mastných kyselin v sledovaných lipidech a mohou souviset s potenciálními kardioprotektivními účinky obou intervencí
Keywords:
heart; chronic hypoxia; lipid diet
Available at various institutes of the ASCR
Effects of dietary polyunsaturated fatty acids on myocardial and serum lipids in normoxic and chronically hypoxic rat heart
The goal of this study was to fellow up the effect of n-3 and n-6 polyunsaturated fatty acids (PUFA) and the adaptation to chronic intermittent hypoxic (CIH) on fatty acid (FA) composition of serum ...
Quantification of Osteocyte Lacunar Density and Anisotropy of Vascular Canals in Compact Bone
Maštálková, K.; Tonar, Z.; Fiala, P.; Janáček, Jiří
2008 - English
Numerical density of osteocyte lacunes in cortex and medula of diaphysis of tibia was estimated using thick sections and disector method. Anisotropy in lacunes localization was proved by a method based on Delaunay triangulation Numerická hustota osteocytů v dřeni a kůře střední části lidské holenní kosti byla odhadnuta z tlustých řezů metodou disektoru. Anizotropie v rozmístění osteocytů byla prokázána metodou založenou na Deloneho triangulaci
Keywords:
osteocyte; disector
Available at various institutes of the ASCR
Quantification of Osteocyte Lacunar Density and Anisotropy of Vascular Canals in Compact Bone
Numerical density of osteocyte lacunes in cortex and medula of diaphysis of tibia was estimated using thick sections and disector method. Anisotropy in lacunes localization was proved by a method ...
Error Assesment of Volume Reconstruction of Biological Specimen from Confocal Microscopy Images
Čapek, Martin; Janáček, Jiří; Kubínová, Lucie; Smrčka, P.; Hána, K.
2008 - English
We performed both volume reconstructions using images captured by the USB microscope and images captured by the confocal microscope. We manually marked important corresponding structures in both reconstructed data sets, and computed distances between corresponding structures, assuming that structures in the reconstruction from USB microscope data are without deformations. According to our expectations, the main errors of high-resolution volume reconstruction (from confocal data) are in the direction of physical cutting (vary in units of millimeters) and in the direction perpendicular to cutting due to off-cut (vary in tenths of millimeters) Objemovou rekonstrukci využíváme pro vizualizaci biologických preparátů, které jsou větší, než je velikost zorného pole a/nebo silnější v tloušťce než je hloubka průniku laserového paprsku konfokálního mikroskopu. Tlusté preparáty je nutno nakrájet na fyzické řezy mikrotomem, avšak krájení způsobuje deformaci a ztrátu části informace prořezem, které vedou k chybám následné objemové rekonstrukce. Pro získání informace o deformaci jsme USB mikroskopem Dino-Lite zaznamenali řezné plochy preparátu zalitého v parafinu před jeho nakrájením, tj. bez deformací. Po nasnímání fyzických řezů vyhodnocujeme chybu deformace pomocí Prokrustovy vzdálenosti, která kvantifikuje střední kvadratickou vzdálenost tvarů vyjádřených pomocí bodů
Keywords:
error assessment; volume reconstruction
Available at various institutes of the ASCR
Error Assesment of Volume Reconstruction of Biological Specimen from Confocal Microscopy Images
We performed both volume reconstructions using images captured by the USB microscope and images captured by the confocal microscope. We manually marked important corresponding structures in both ...
Tools for visualization of large three-dimensional objects in biology
Čapek, Martin; Janáček, Jiří; Kubínová, Lucie; Smrčka, P.; Hána, K.
2007 - English
Three-dimensional images of biological objects or structures recorded by modern acquisition tools like a confocal laser scanning microscope are visualized for their evaluation, analysis and measurement. We report about possibilities for three-dimensional visualization which are offered by either our Rapid3D software package suited for three-dimensional reconstruction and visualization of bio-medical images or Ellipse modular software package devoted to biological image processing (ViDiTo company, Slovakia) 3D obrazy biologických objektů nebo struktur jsou získávány pomocí moderních zobrazovacích zařízení jako je například konfokální laserový rastrovací mikroskop pro jejich ohodnocení, analýzu nebo měření. Reportujeme o možnostech vizualizace 3D skalárních obrazů pomocí našeho programového prostředí Rapid3D určeného pro objemovou rekonstrukci a vizualizaci biomedicínských obrazů nebo pomocí modulárního softwaru Ellipse určeného pro zpracování biologických obrazů
Keywords:
3D visualization; confocal microscopy
Available at various institutes of the ASCR
Tools for visualization of large three-dimensional objects in biology
Three-dimensional images of biological objects or structures recorded by modern acquisition tools like a confocal laser scanning microscope are visualized for their evaluation, analysis and ...
LP-12 Approaches to visualization of 3D structures captured by a confocal microscope
Čapek, Martin; Janáček, Jiří; Kubínová, Lucie; Hána, K.; Smrčka, P.
2007 - English
Laser scanning confocal microscopes are capable to focus a laser beam into a layer of an investigated biological specimen, and by the gradual scanning of this layer they acquire an optical section. By consecutive scanning of all preset layers of the specimen we obtain a stack of optical sections, i.e. a 3D digital representation of the specimen. In the presented study we focus on volume reconstruction of large biological tissues, i.e. tissues greater than field of view and/or thicker than maximal depth of scanning of a confocal microscope. As a result of volume reconstruction we obtain a high resolution 3D image of the biological specimen. 3D visualization is offered either by our Rapid3D software package suited for three-dimensional reconstruction and visualization of biomedical images, or Ellipse modular software package devoted to biological image processing (created by ViDiTo company, Slovakia) Článek popisuje přístupy k objemové rekonstrukci a vizualizaci 3D biologických struktur nasnímaných konfokálním mikroskopem
Keywords:
confocal microscopy; volume visualization
Available at various institutes of the ASCR
LP-12 Approaches to visualization of 3D structures captured by a confocal microscope
Laser scanning confocal microscopes are capable to focus a laser beam into a layer of an investigated biological specimen, and by the gradual scanning of this layer they acquire an optical section. By ...
Tools for 3D Visualization of Structures in Biology
Čapek, Martin; Janáček, Jiří; Kubínová, Lucie; Smrčka, P.; Hána, K.
2007 - English
By consecutive scanning of layers of the biological specimen by a confocal microscope we obtain a stack of optical sections, i.e. a 3D digital representation of the specimen. Our research focuses, on volume reconstruction of large biological tissues, i.e. tissues greater than field of view and/or thicker than maximal depth of scanning of the confocal microscope. As a result of volume reconstruction we obtain a high resolution 3D image of the biological specimen. In order to visualize 3D objects on 2D computer screens we developed several tools including visualization by a specialized VolumePro board and by using consumer graphics cards supporting DirectX and OpenGL Článek popisuje prostředky pro vizualizaci trojrozměrných skalárních dat získaných laserovým konfokálním mikroskopem z velkých biologických vzorků. Těmito prostředky jsou programy využívající PC kartu VolumePro firmy Terarecon, USA a běžné grafické karty podporující DirectX a OpenGL
Keywords:
3D visualization; OpenGL; DirectX
Available at various institutes of the ASCR
Tools for 3D Visualization of Structures in Biology
By consecutive scanning of layers of the biological specimen by a confocal microscope we obtain a stack of optical sections, i.e. a 3D digital representation of the specimen. Our research focuses, on ...
Volume visualization of large biological tissue specimens
Čapek, Martin; Kubínová, Lucie; Janáček, Jiří; Hána, K.; Smrčka, P.
2006 - English
We apply volume reconstruction for visualization of a biological specimen greater than the field of view of a confocal laser scanning microscope. Prior to the volume reconstruction, large specimens are cut into thin physical slices. The first step of volume reconstruction is acquisition of digital volume images (spatial tiles which overlap) from all studied physical slices. The second step is horizontal merging of overlapping spatial tiles of the same physical slice using a registration algorithm based on a mutual information and translation. The third reconstruction step is vertical merging of digital volumes of successive physical slices using an elastic registration algorithm based on B-splines. The resulting large digital volumes are visualized by a VolumePro hardware board that provides volume rendering in real-time. In this paper we show a reconstruction of a chick embryonic kidney. Objemová vizualizace velkých biologických tkáňových vzorků se skládá z následujících kroků: nařezání preparátu na tenké fyzické řezy, nasnímání překrývajících se obrazových dat z fyzických řezů, horizontální skládání překrývajících se obrazových dat s použitím registrace do 3D sub-obrazu reprezentující jeden fyzický řez, vertikální skládání sub-obrazů fyzických řezů s použitím elastické registrace do výsledné 3D reprezentace biologického preparátu a vizualizace 3D obrazu s využitím VolumePro hardware
Keywords:
confocal microscopy; volume reconstruction
Available at various institutes of the ASCR
Volume visualization of large biological tissue specimens
We apply volume reconstruction for visualization of a biological specimen greater than the field of view of a confocal laser scanning microscope. Prior to the volume reconstruction, large specimens ...
Vizualization of large biological tissue specimens using confocal laser scanning microscopy
Čapek, Martin; Kubínová, Lucie; Hána, K.; Smrčka, P.
2006 - English
In biology there is often necessary to visualize a biological specimen which size is greater when compared with the field of view of a used optical acquisition instrument. The visualization of such the specimen can be achieved by volume reconstruction. We study biological specimens by using a confocal laser scanning microscope which is able to capture a digital volume representation of the specimen. We investigate great specimens containing, for example, a human tooth pulp, an epithelial layer and a vascular bed of chick embryonic gut or chick embryonic kidneys Objemová rekonstrukce je metoda sloužící k vizualizaci trojrozměrné struktury biologických vzorků, jejichž velikost může být větší než je horizontální či axiální zorné pole snímacího systému (v našem případě laserového konfokálního mikroskopu). Velké vzorky je nutné nařezat na tenké fyzické řezy. Pak se snímají všechny sousedící a překrývající se objemové obrazy v rámci jednotlivých fyzických řezů (kompenzace omezeného horizontálního zorného pole). Takové sousedící obrazy se dále získají pro všechny sériové fyzické řezy (kompenzace omezeného axiálního zorného pole)
Keywords:
confocal microscopy; volume reconstruction; volume visualization
Available at various institutes of the ASCR
Vizualization of large biological tissue specimens using confocal laser scanning microscopy
In biology there is often necessary to visualize a biological specimen which size is greater when compared with the field of view of a used optical acquisition instrument. The visualization of such ...
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