Large Image Stacks Research Articles

Informatics in Radiology: Hesse Rendering for Computer-aided Visualization and Analysis of Anomalies at Chest CT and Breast MR Imaging

A volume-rendering (VR) technique known as Hesse rendering applies image-enhancement filters to three-dimensional imaging volumes and depicts the filter responses in a color-coded fashion. Unlike direct VR, which makes use of intensities, Hesse rendering operates on the basis of shape properties, such that nodular structures in the resulting renderings have different colors than do tubular structures and thus are easily visualized. The renderings are mouse-click sensitive and can be used to navigate to locations of possible anomalies in the original images. Hesse rendering is meant to complement rather than replace conventional section-by-section viewing or VR. Although it is a pure visualization technique that involves no internal segmentation or explicit object detection, Hesse rendering, like computer-aided detection, may be effective for quickly calling attention to points of interest in large stacks of images and for helping radiologists to avoid oversights.

Espina: A Tool for the Automated Segmentation and Counting of Synapses in Large Stacks of Electron Microscopy Images

The synapses in the cerebral cortex can be classified into two main types, Gray's type I and type II, which correspond to asymmetric (mostly glutamatergic excitatory) and symmetric (inhibitory GABAergic) synapses, respectively. Hence, the quantification and identification of their different types and the proportions in which they are found, is extraordinarily important in terms of brain function. The ideal approach to calculate the number of synapses per unit volume is to analyze 3D samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using focused ion beam/scanning electron microscope microscopy, we recently showed that virtually all synapses can be accurately identified as asymmetric or symmetric synapses when they are visualized, reconstructed, and quantified from large 3D tissue samples obtained in an automated manner. Nevertheless, the analysis, segmentation, and quantification of synapses is still a labor intensive procedure. Thus, novel solutions are currently necessary to deal with the large volume of data that is being generated by automated 3D electron microscopy. Accordingly, we have developed ESPINA, a software tool that performs the automated segmentation and counting of synapses in a reconstructed 3D volume of the cerebral cortex, and that greatly facilitates and accelerates these processes.

Interactive Histology of Large-Scale Biomedical Image Stacks

Histology is the study of the structure of biological tissue using microscopy techniques. As digital imaging technology advances, high resolution microscopy of large tissue volumes is becoming feasible; however, new interactive tools are needed to explore and analyze the enormous datasets. In this paper we present a visualization framework that specifically targets interactive examination of arbitrarily large image stacks. Our framework is built upon two core techniques: display-aware processing and GPU-accelerated texture compression. With display-aware processing, only the currently visible image tiles are fetched and aligned on-the-fly, reducing memory bandwidth and minimizing the need for time-consuming global pre-processing. Our novel texture compression scheme for GPUs is tailored for quick browsing of image stacks. We evaluate the usability of our viewer for two histology applications: digital pathology and visualization of neural structure at nanoscale-resolution in serial electron micrographs.

Polarimetric Characterization and Temporal Stability Analysis of Urban Target Scattering

This paper studies the polarimetric-dispersion properties of urban targets and their evolution along time in terms of the geometrical configuration. The relations between target geometry and the scattering behavior have been defined through the analysis of large stacks of simulated images. Scattering maps and synthetic aperture radar (SAR) images have been synthesized with the numerical tool GRaphical Electromagnetic COmputing SAR for different qualitative models of two real buildings. Ground-based SAR (GB-SAR) data acquired in a subsidence measurement campaign has been used to assess the simulator's realism. These data have permitted the identification of the critical simulation parameters and their range of recommended values for realistic simulations. In the context of very high resolution images, the results derived from this study may be crucial for making progress in urban-image postprocessing. As the different resolution cells comprise few scattering centers showing a quasi-deterministic scattering behavior, nonprobabilistic models based on target's geometry seem more suited for scattering modeling. In these models, the geometry-scattering (GS) links precisely inferred from simulated images can be very important. In addition to change detection and land classification, GS models may help in improving the interpretation of subsidence results with differential interferometry. Certainly, new processing algorithms can be developed exploiting the available scattering data with more physical sense. In addition, they can take more advantage of the fine resolution and polarimetric capabilities of the new sensors, like TerraSAR-X or RADARSAT-2.

CATMAID: collaborative annotation toolkit for massive amounts of image data

Summary: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps™, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy.Availability: http://fly.mpi-cbg.de/catmaidContact: tomancak@mpi-cbg.de

Christian Chromolithographs in Ethiopia

Briana B. Simmons The Ethiopian Orthodox Church (EOC) has produced iconographic religious painting since the sixth century ce, but with the onset of mechanical reproduction and faster printing technologies, worshippers now have access to new types of religious images.1 Today, foreign and locally produced chromolithographic images (or color prints) depicting Christian religious figures are readily available in Ethiopia and have become one of the most popular and prevalent art forms in the country. This is due in part to their high volume but also to their variety, malleability, and relatively low price, which places them into a category of decorative and ritually important objects that most Orthodox Ethiopians desire. Images such as Figure 1, of the Virgin and Child, generally depict Biblical figures that are copied from historical Western paintings or drawings. This research note outlines how Ethiopian Orthodox Christians use these religious images and briefly addresses their effect on the construction of an Orthodox identity.2 I will also discuss how church-trained painters have responded to these images and what the influx of chromolithographs has meant for their business. These reproduced images are part of a continual process of adaptation and change in the religious practices of Ethiopian Orthodox Christians. Rather than dismissing them as kitsch or artistic degeneration, this study examines how they are used as aesthetic objects and the value they hold for the Christian faithful. For this note, “chromolithograph” refers to any color print displayed in Ethiopia that is mechanically produced in Ethiopia or abroad. This comprehensive definition includes a number of printing technologies, ranging from traditional chromolithography to more modern photo offset printing processes. The prints can be purchased for one or two birr, which is approximately 10 to 20 US cents, and they are sold on sidewalks, especially outside Ethiopian Orthodox churches. Vendors often set up open-air stalls to exhibit the images, sometimes using upturned umbrellas to easily display numerous prints. It is common for peddlers to traverse local neighborhoods on foot carrying large stacks of images for sale. The prints range in size from small, 3 x 4 cards to large posters that are several feet across.3 Several scholars have examined the use of religious and secular chromolithographs in other countries (Jain 2007, Cosentino 2005, Pinney 1997, 2004, Rush 1999), but only one general overview of chromolithograph use in Ethiopia exists (Silverman, in All photos Are by the Author

Interactive visualization of multiresolution image stacks in 3D

Conventional microscopy, electron microscopy, and imaging techniques such as MRI and PET commonly generate large stacks of images of the sectioned brain. In other domains, such as neurophysiology, variables such as space or time are also varied along a stack axis. Digital image sizes have been progressively increasing and in virtual microscopy, it is now common to work with individual image sizes that are several hundred megapixels and several gigabytes in size. The interactive visualization of these high-resolution, multiresolution images in 2D has been addressed previously [Sullivan, G., and Baker, R., 1994. Efficient quad-tree coding of images and video. IEEE Trans. Image Process. 3 (3), 327–331]. Here, we describe a method for interactive visualization of multiresolution image stacks in 3D.The method, characterized as quad-tree based multiresolution image stack interactive visualization using a texel projection based criterion, relies on accessing and projecting image tiles from multiresolution image stacks in such a way that, from the observer's perspective, image tiles all appear approximately the same size even though they are accessed from different tiers within the images comprising the stack. This method enables efficient navigation of high-resolution image stacks. We implement this method in a program called StackVis, which is a Windows-based, interactive 3D multiresolution image stack visualization system written in C++ and using OpenGL. It is freely available at http://brainmaps.org.

Early detection and in-depth analysis of deformation phenomena by radar interferometry

The spaceborne differential interferometric SAR (DInSAR) technique may play an important role in the measurement of land deformation phenomena, especially in urban, suburban and industrial areas. In order to fully exploit its capabilities and increase its operational use, this paper proposes two complementary levels of analysis. The first one is a comprehensive low-cost screening, in order to detect unknown subsidence phenomena over large areas. This analysis, which provides a first estimation of deformations, has to be performed using a limited set of SAR images. The second level includes an in-depth quantitative analysis based on large image stacks, which requires more image acquisition and data processing resources. This type of analysis can be typically used to study deformation phenomena of special relevance, where an effective support to the decision-makers requires a fully quantitative estimation of deformations. The two levels of analysis were proved over a test area of about 2100 km 2, located in Catalonia (Spain). Without any a priori information, seven deformation phenomena were detected using a reduced set of interferograms. Furthermore, the quantitative analysis of a subsidence of small spatial extent, which was based on ascending and descending datasets, confirmed the capability of DInSAR to quantitatively assess deformation phenomena.