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Elastic registration of biomedical images on CUDA-Supported graphics procesor units
Michálek, Jan ; Čapek, Martin ; Janáček, Jiří ; Kubínová, Lucie
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
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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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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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Vizualizace velkých biologických tkáňových vzorků s použitím laserové konfokální mikroskopie
Čapek, Martin ; Kubínová, Lucie ; Hána, K. ; Smrčka, P.
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
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