TY - GEN A1 - Baum, Daniel T1 - An Evaluation of Color Maps for Visual Data Exploration T3 - ZIB-Report - 19-42 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74259 SN - 1438-0064 ER - TY - GEN A1 - Baum, Daniel A1 - Weaver, James C. A1 - Zlotnikov, Igor A1 - Knötel, David A1 - Tomholt, Lara A1 - Dean, Mason N. T1 - High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms N2 - Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e. poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e. structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, this random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—stingray tessellated cartilage, starfish dermal endoskeleton, and the prismatic layer of bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized and analyzed. T3 - ZIB-Report - 19-33 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73841 SN - 1438-0064 ER - TY - GEN A1 - Baum, Daniel A1 - Giliard, Nicole A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang T1 - Leitlinien zum Umgang mit Forschungsdaten am Zuse-Institut Berlin N2 - Die nachhaltige Sicherung und Bereitstellung von Forschungsdaten dienen nicht nur der Reproduzierbarkeit früherer Ergebnisse, sondern in hohem Maße auch der Erzielung künftiger Ergebnisse mit dem Ziel, die Qualität, Produktivität und Wettbewerbsfähigkeit der Wissenschaft zu fördern. Die folgenden Grundsätze gelten als Leitlinien zur Handhabung von Forschungsdaten im ZIB. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73781 CY - Berlin ER - TY - GEN A1 - Mahnke, Heinz-Eberhard A1 - Arlt, Tobias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Herter, Felix A1 - Lindow, Norbert A1 - Manke, Ingo A1 - Siopi, Tzulia A1 - Menei, Eve A1 - Etienne, Marc A1 - Lepper, Verena T1 - Virtual unfolding of folded papyri N2 - The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Musée du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for “Lord”. T3 - ZIB-Report - 19-44 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74338 SN - 1438-0064 ER -