Oleg Lobachev

Parallel FFT with Eden Skeletons

The paper investigates and compares skeleton-based Eden implementations of different FFT-algorithms on workstation clusters with distributed memory. Our experiments show that the basic divide-and-conquer versions suffer from an inherent input distribution and result collection problem. Advanced approaches like calculating FFT using a parallel map-and-transpose skeleton provide more flexibility to overcome these problems. Assuming a distributed access to input data and re-organising computation to return results in a distributed way improves the parallel runtime behaviour.

Feature-based multi-resolution registration of immunostained serial sections.

&NA; The form and exact function of the blood vessel network in some human organs, like spleen and bone marrow, are still open research questions in medicine. In this paper, we propose a method to register the immunohistological stainings of serial sections of spleen and bone marrow specimens to enable the visualization and visual inspection of blood vessels. As these vary much in caliber, from mesoscopic (millimeter‐range) to microscopic (few micrometers, comparable to a single erythrocyte), we need to utilize a multi‐resolution approach. Our method is fully automatic; it is based on feature detection and sparse matching. We utilize a rigid alignment and then a non‐rigid deformation, iteratively dealing with increasingly smaller features. Our tool pipeline can already deal with series of complete scans at extremely high resolution, up to 620 megapixels. The improvement presented increases the range of represented details up to smallest capillaries. This paper provides details on the multi‐resolution non‐rigid registration approach we use. Our application is novel in the way the alignment and subsequent deformations are computed (using features, i.e. “sparse”). The deformations are based on all images in the stack (“global”). We also present volume renderings and a 3D reconstruction of the vascular network in human spleen and bone marrow on a level not possible before. Our registration makes easy tracking of even smallest blood vessels possible, thus granting experts a better comprehension. A quantitative evaluation of our method and related state of the art approaches with seven different quality measures shows the efficiency of our method. We also provide z‐profiles and enlarged volume renderings from three different registrations for visual inspection. HighlightsWe non‐rigidly register immunohistological serial sections of human specimen.Using feature detection and matching we iteratively compute non‐rigid deformations.Vascular networks in spleen and bone marrow are shown on a level not possible before.A quantitative evaluation of our method shows its efficiency. Graphical abstract Figure. No caption available.

Imaging the vascular network of the human spleen from immunostained serial sections

The spleen is one of the organs, where the micro-structure and the function on that level are not completely understood. It was for example only recently found that is has an open circulation, which distinguishes it from all other organs. Imaging the complete vascular network from the arteries to open-ended capillaries would greatly facilitate research in this area. The structure of such tissue is best uncovered using immunehistological staining. This can however only be applied to thin tissue sections and larger structures span several slices. Due to the deformation induced when cutting the specimen, standard registration algorithms cannot be used to merge the images into a volume. We propose a specialized matching algorithm to robustly determine corresponding regions in the images. After a rigid alignment of the scans, we use a cubic B-spline to deform and align the images. During this process we minimize the total deformation to produce as accurate results as possible.

Parallel computation skeletons with premature termination property

A parallel computation with early termination property is a special form of a parallel for loop. This paper devises a generic highlevel approach for such computation which is expressed as a scheme for algorithmic skeletons. We call this scheme map+reduce , in similarity with the map-reduce paradigm. The implementation is concise and relies heavily on laziness. Two case studies from computational number theory support our presentation.

Capillary networks and follicular marginal zones in human spleens : Three-dimensional models based on immunostained serial sections

We have reconstructed small parts of capillary networks in the human splenic white pulp using serial sections immunostained for CD34 alone or for CD34 and CD271. The three-dimensional (3D) models show three types of interconnected networks: a network with very few long capillaries inside the white pulp originating from central arteries, a denser network surrounding follicles plus periarterial T-cell regions and a network in the red pulp. Capillaries of the perifollicular network and the red pulp network have open ends. Perifollicular capillaries form an arrangement similar to a basketball net located in the outer marginal zone. The marginal zone is defined by MAdCAM-1+ marginal reticular stromal cells. Perifollicular capillaries are connected to red pulp capillaries surrounded by CD271+ stromal capillary sheath cells. The scarcity of capillaries inside the splenic white pulp is astonishing, as non-polarised germinal centres with proliferating B-cells occur in adult human spleens. We suggest that specialized stromal marginal reticular cells form a barrier inside the splenic marginal zone, which together with the scarcity of capillaries guarantees the maintenance of gradients necessary for positioning of migratory B- and T-lymphocytes in the human splenic white pulp.

Three-Dimensional Arrangement of Human Bone Marrow Microvessels Revealed by Immunohistology in Undecalcified Sections

The arrangement of microvessels in human bone marrow is so far unknown. We combined monoclonal antibodies against CD34 and against CD141 to visualise all microvessel endothelia in 21 serial sections of about 1 cm2 size derived from a human iliac crest. The specimen was not decalcified and embedded in Technovit® 9100. In different regions of interest, the microvasculature was reconstructed in three dimensions using automatic methods. The three-dimensional models were subject to a rigid semiautomatic and manual quality control. In iliac crest bone marrow, the adipose tissue harbours irregularly distributed haematopoietic areas. These are fed by networks of large sinuses, which are loosely connected to networks of small capillaries prevailing in areas of pure adipose tissue. Our findings are compatible with the hypothesis that capillaries and sinuses in human iliac crest bone marrow are partially arranged in parallel.

Direct Visualization of Cryptographic Keys for Enhanced Security

PGP public keys are relatively small binary data. Their hashes are used and also visualized for comparison and validation purposes. We pursue a direct, but previously unused approach. We produce colorful images of public keys and other binary data by generating drawing primitives from binary input. Optionally, we also include the hashes in the visualization. The visualization of raw data together with its hash provides a further security benefit. With it we can visually detect hash collisions. The primary focus of this paper is a direct visualization of public keys. We tune the transparency heuristics for better results. Our method visually detects key spoofing on real SHA1 collision data.