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Ohodnocení chyby objemové rekonstrukce biologických vzorků z konfokálních obrazů
Čapek, Martin ; Janáček, Jiří ; Kubínová, Lucie ; Smrčka, P. ; Hána, K.
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)
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Přístupy k visualizaci obrazů 3D struktur získaných konfokálním mikroskopem
Čapek, Martin ; Janáček, Jiří ; Kubínová, Lucie ; Hána, K. ; Smrčka, P.
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)
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Nástroje pro trojrozměrnou vizualizaci struktur v biologii
Čapek, Martin ; Janáček, Jiří ; Kubínová, Lucie ; Smrčka, P. ; Hána, K.
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
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Objemová rekonstrukce velkých biologických tkáňových vzorků
Čapek, Martin ; Janáček, Jiří ; Kubínová, Lucie ; Smrčka, P. ; Hána, K.
Volume reconstruction is a technique for visualization of a biological specimen which is greater than the field of view of a used optical instrument - a confocal laser scanning microscope in our case. The first step of volume reconstruction is acquisition of sets 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 (mosaicking). The third reconstruction step is vertical merging of digital volumes of successive physical slices of the specimen. The resulting large digital volumes are visualized using a VolumePro hardware board that offers real-time 3D volume rendering. In this paper we show a reconstruction of a chick embryonic kidney
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Objemová vizualizace velkých biologických tkáňových vzorků
Čapek, Martin ; Kubínová, Lucie ; Janáček, Jiří ; Hána, K. ; Smrčka, P.
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.
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3D vizualizace velkých biologických vzorků nasnímaných konfokálním mikroskopem
Čapek, Martin ; Janáček, Jiří ; Karen, Petr ; Kubínová, Lucie ; Smrčka, P. ; Hána, K.
Digital volume reconstruction is a technique for rendering and visualization of a biological specimen which is greater than the field of view of a used optical instrument - a confocal laser scanning microscope in our case. Prior to the volume reconstruction, large biological specimens are cut to thin physical slices. The first step of volume reconstruction is acquisition of sets of digital volume images (spatial tiles which overlap) from all studied physical slices. The second step is composition of neighbouring spatial tiles of the same physical slice. The third reconstruction step is registration and merging of digital volumes of neighbouring physical slices of the specimen. The resulting large digital volumes are rendered and visualized using a VolumePro hardware board that offers real-time 3D volume rendering. In this paper we show a reconstruction of a chick embryonic kidney
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