Fast and Accurate Camera Covariance Computation for Large 3D Reconstruction

Estimating uncertainty of camera parameters computed in Structure from Motion (SfM) is an important tool for evaluating the quality of the reconstruction and guiding the reconstruction process. Yet, the quality of the estimated parameters of large reconstructions has been rarely evaluated due to the computational challenges. We present a new algorithm which employs the sparsity of the uncertainty propagation and speeds the computation up about ten times \wrt previous approaches. Our computation is accurate and does not use any approximations. We can compute uncertainties of thousands of cameras in tens of seconds on a standard PC. We also demonstrate that our approach can be effectively used for reconstructions of any size by applying it to smaller sub-reconstructions.Comment: ECCV 201

Subobject Detection through Spatial Relationships on Mobile Phones

We present a novel image classification technique for detecting multiple objects (called subobjects) in a single image. In addition to image classifiers, we apply spatial relationships among the subobjects to verify and to predict locations of detected and undetected subobjects, respectively. By continuously refining the spatial relationships throughout the detection process, even locations of completely occluded exhibits can be determined. Finally, all detected subobjects are labeled and the user can select the object of interest for retrieving corresponding multimedia information. This approach is applied in the context of PhoneGuide, an adaptive museum guidance system for camera-equipped mobile phones. We show that the recognition of subobjects using spatial relationships is up to 68% faster than related approaches without spatial relationships. Results of a field experiment in a local museum illustrate that unexperienced users reach an average recognition rate for subobjects of 85.6% under realistic conditions

BAT (Berry Analysis Tool): A high-throughput image interpretation tool to acquire the number, diameter, and volume of grapevine berries

QTL-analysis (quantitative trait loci) and marker development rely on efficient phenotyping techniques. Objectivity and precision of a phenotypic data evaluation is crucial but time consuming. In the present study a high-throughput image interpretation tool was developed to acquire automatically number, size, and volume of grape berries from RGB (red-green-blue) images. Individual berries of one cluster were placed on a black construction (300 x 300 mm) to take a RGB image from the top. The image interpretation of one dataset with an arbitrary number of images runs automatically using the BAT (Berry-Analysis-Tool) developed in MATLAB. For validation of results, the number of berries was counted and their size was measured using a digital calliper. A measuring cylinder was used to determine reliably the berry volume by displacement of water. All placed berries could be counted by BAT 100 % correctly. Manual ratings compared with BAT ratings showed strong correlation of r = 0.96 for mean berry diameter/image and r = 0.98 for cluster volume.

Initial steps for high-throughput phenotyping in vineyards

The evaluation of phenotypic characters of grapevines is required directly in vineyards and is strongly limited by time, costs and the subjectivity of person in charge. Sensor-based techniques are prerequisite in order to allow non-invasive phenotyping of individual plant traits, to increase the quantity of object records and to reduce error variation. Thus, a Prototype-Image-Acquisition-System (PIAS) was developed for semi-automated capture of geo-referenced images in an experimental vineyard. Different strategies were tested for image interpretation using MATLAB®. The interpretation of images from the vineyard with real background is more practice-oriented but requires the calculation of depth maps. Different image analysis tools were verified in order to enable contactless and non-invasive detection of bud burst and quantification of shoots at an early developmental stage (BBCH 10) and enable fast and accurate determination of the grapevine berry size at BBCH 89. Depending on the time of image acquisition at BBCH 10 up to 94 % of green shoots were visible in images. The mean berry size (BBCH 89) was recorded non-invasively with a precision of 1 mm.

Surface velocity fields of active rock glaciers and ice-debris complexes in the Central Andes of Argentina

Rock glaciers and transitional ice-debris complexes predominate the Central Andean landform assemblage, yet regional studies on their state of activity and their kinematics remain sparse. Here we utilize the national glacier inventory of Argentina to quantify surface velocity fields of 244 rock glaciers and 51 ice-debris complexes, located in the Cordón del Plata range, Argentina. Applying a feature-tracking approach to repeated RapidEye satellite imagery acquired between 2010 and 2017/18, we find mean displacement rates between 0.37 and 2.61 m year−1 for 149 landforms, while for the remaining 146 features, surface movement remains below our level of detection. We compare our satellite-derived velocity fields with ground-truth data from two local field sites and find closely matching results in magnitude and spatial distribution. With average displacement of one-third of the active rock glaciers and ice-debris complexes exceeding 1 m year−1, the region hosts an exceptional number of fast-flowing periglacial landforms, compared to other mountain belts. Using a random forest model, we test the predictive power of 25 morphometric and topoclimatic candidate predictors for modelling the state of activity of rock glaciers and ice-debris complexes on two different scales. For entire landforms and individual landform segments, constructed along displacement centrelines, we can predict the state of activity with overall accuracies of 70.08% (mean AUROC = 0.785) and 74.86% (mean AUROC = 0.753), respectively. While topoclimatic parameters such as solar radiation and elevation are most important for entire landforms, geometric parameters become more important at the scale of landform segments. Despite tentative correlations between local slope and surface kinematics, our results point to factors integrating slope and distance to the source to govern local deformation. We conclude that feature tracking in optical imagery is feasible for regional studies in remote regions and provides valuable insight into the current state of the Andean cryosphere.Fil: Blöthe, Jan Henrik. Universitat Bonn; AlemaniaFil: Halla, Christian. Universitat Bonn; AlemaniaFil: Schwalbe, Ellen. Technische Universität Dresden; AlemaniaFil: Bottegal, Estefania Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Trombotto, Dario Tomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Schrott, Lothar. Universitat Bonn; Alemani

Tensor voting for robust color edge detection

The final publication is available at Springer via http://dx.doi.org/10.1007/978-94-007-7584-8_9This chapter proposes two robust color edge detection methods based on tensor voting. The first method is a direct adaptation of the classical tensor voting to color images where tensors are initialized with either the gradient or the local color structure tensor. The second method is based on an extension of tensor voting in which the encoding and voting processes are specifically tailored to robust edge detection in color images. In this case, three tensors are used to encode local CIELAB color channels and edginess, while the voting process propagates both color and edginess by applying perception-based rules. Unlike the classical tensor voting, the second method considers the context in the voting process. Recall, discriminability, precision, false alarm rejection and robustness measurements with respect to three different ground-truths have been used to compare the proposed methods with the state-of-the-art. Experimental results show that the proposed methods are competitive, especially in robustness. Moreover, these experiments evidence the difficulty of proposing an edge detector with a perfect performance with respect to all features and fields of application.This research has been supported by the Swedish Research Council under the project VR 2012-3512

Measurement of Acid Volatile Sulphide and Simultaneously Extracted Metals in Sediment from Lake Albufera (Valencia, Spain)

Lake Albufera (Valencia, Spain) is part of a legally protected wetland of international importance. However, it has deteriorated as a result of urban, industrial, and farming pollution. It is highly eutrophic, and its sediment contains persistent pollutants, such as heavy metals. In anoxic sediments, sulphides represent an important binding phase for heavy metals. In this study, acid volatile sulphide (AVS) and simultaneously extracted metals (SEM) were analyzed in surface sediment extracted from Lake Albufera; organic matter and total metals were also analyzed. Twelve sites were sampled in each of three sampling campaigns conducted in March and September 2007 and September 2008. The results revealed elevated organic matter contents varying between 6.9 and 16.7%. The concentrations of AVS in the lake were high, ranging from 8.5 to 48.5 ¿mol/g; the lowest concentrations were found in the central sites. The AVS results displayed significant differences between the samples from the winter and summer of 2007 (p < 0.05) but not between the two summer samples. The results obtained for SEM varied from 1.4 to 4.8 ¿mol/g. The difference SEM-AVS was less than zero for all sampling locations and campaigns, indicating the existence of a sulphide pool able to bind metals. © 2012 Copyright Taylor and Francis Group, LLC.Hernández Crespo, C.; Martín Monerris, M.; Ferris Juan, M.; Oñate Ema, M. (2012). Measurement of Acid Volatile Sulphide and Simultaneously Extracted Metals in Sediment from Lake Albufera (Valencia, Spain). Soil and Sediment Contamination. 21(2):176-191. doi:10.1080/15320383.2012.649374S176191212Allen, H. E., Fu, G., & Deng, B. (1993). Analysis of acid-volatile sulfide (AVS) and simultaneously extracted metals (SEM) for the estimation of potential toxicity in aquatic sediments. Environmental Toxicology and Chemistry, 12(8), 1441-1453. doi:10.1002/etc.5620120812Besser, J. M., Brumbaugh, W. G., Ivey, C. D., Ingersoll, C. G., & Moran, P. W. (2007). Biological and Chemical Characterization of Metal Bioavailability in Sediments from Lake Roosevelt, Columbia River, Washington, USA. Archives of Environmental Contamination and Toxicology, 54(4), 557-570. doi:10.1007/s00244-007-9074-5Burton, G. A., Green, A., Baudo, R., Forbes, V., Nguyen, L. T. H., Janssen, C. R., … Dunning, J. (2007). CHARACTERIZING SEDIMENT ACID VOLATILE SULFIDE CONCENTRATIONS IN EUROPEAN STREAMS. Environmental Toxicology and Chemistry, 26(1), 1. doi:10.1897/05-708r.1Casado-Martínez, M. C., Buceta, J. L., Belzunce, M. J., & DelValls, T. A. (2006). Using sediment quality guidelines for dredged material management in commercial ports from Spain. Environment International, 32(3), 388-396. doi:10.1016/j.envint.2005.09.003Choi, J. H., Park, S. S., & Jaffé, P. R. (2006). Simulating the dynamics of sulfur species and zinc in wetland sediments. Ecological Modelling, 199(3), 315-323. doi:10.1016/j.ecolmodel.2006.05.009De Jonge, M., Blust, R., & Bervoets, L. (2010). The relation between Acid Volatile Sulfides (AVS) and metal accumulation in aquatic invertebrates: Implications of feeding behavior and ecology. Environmental Pollution, 158(5), 1381-1391. doi:10.1016/j.envpol.2010.01.001De Lange, H. J., Van Griethuysen, C., & Koelmans, A. A. (2008). Sampling method, storage and pretreatment of sediment affect AVS concentrations with consequences for bioassay responses. Environmental Pollution, 151(1), 243-251. doi:10.1016/j.envpol.2007.01.052Di Toro, D. M., Mahony, J. D., Hansen, D. J., Scott, K. J., Carlson, A. R., & Ankley, G. T. (1992). Acid volatile sulfide predicts the acute toxicity of cadmium and nickel in sediments. Environmental Science & Technology, 26(1), 96-101. doi:10.1021/es00025a009Du Laing, G., Rinklebe, J., Vandecasteele, B., Meers, E., & Tack, F. M. G. (2009). Trace metal behaviour in estuarine and riverine floodplain soils and sediments: A review. Science of The Total Environment, 407(13), 3972-3985. doi:10.1016/j.scitotenv.2008.07.025European Union. 2000. “Directive 2000/60/EC of the European Parliament and of the Council establishing a framework for the Community action in the field of water policy”. EU Water Framework Directive. OJ L 327 on 22 December 2000Fang, T., Li, X., & Zhang, G. (2005). Acid volatile sulfide and simultaneously extracted metals in the sediment cores of the Pearl River Estuary, South China. Ecotoxicology and Environmental Safety, 61(3), 420-431. doi:10.1016/j.ecoenv.2004.10.004Grabowski, L. A., Houpis, J. L. J., Woods, W. I., & Johnson, K. A. (2001). Seasonal bioavailability of sediment-associated heavy metals along the Mississippi river floodplain. Chemosphere, 45(4-5), 643-651. doi:10.1016/s0045-6535(01)00037-6Hernández-Crespo, C., Martín, M., Ferrís, M., Oñate, M. and Torán, M. 2010. “Spatial variation of Acid Volatile Sulfide (AVS) and Simultaneously Extracted Metals (SEM) in sediments from Beniarrés, Amadorio and Guadalest reservoirs (Alicante, Spain)”. Seville, Spain: 20th SETAC Europe Annual Meeting. Science and Technology for Environmental Protection.Jingchun, L., Chongling, Y., Spencer, K. L., Ruifeng, Z., & Haoliang, L. (2010). The distribution of acid-volatile sulfide and simultaneously extracted metals in sediments from a mangrove forest and adjacent mudflat in Zhangjiang Estuary, China. Marine Pollution Bulletin, 60(8), 1209-1216. doi:10.1016/j.marpolbul.2010.03.029Lee, J., Lee, B., Yoo, H., Koh, C., & Luoma, S. (2001). Influence of reactive sulfide (AVS) and supplementary food on Ag, Cd and Zn bioaccumulation in the marine polychaete Neanthes arenaceodentata. Marine Ecology Progress Series, 216, 129-140. doi:10.3354/meps216129Lee, J.-S., Lee, B.-G., Luoma, S. N., & Yoo, H. (2004). IMPORTANCE OF EQUILIBRATION TIME IN THE PARTITIONING AND TOXICITY OF ZINC IN SPIKED SEDIMENT BIOASSAYS. Environmental Toxicology and Chemistry, 23(1), 65. doi:10.1897/03-176Leonard, E. N., Mattson, V. R., Benoit, D. A., Hoke, R. A., & Ankley, G. T. (1993). Seasonal variation of acid volatile sulfide concentration in sediment cores from three northeastern Minnesota lakes. Hydrobiologia, 271(2), 87-95. doi:10.1007/bf00007545Longhi, D., Bartoli, M., & Viaroli, P. (2008). Decomposition of four macrophytes in wetland sediments: Organic matter and nutrient decay and associated benthic processes. Aquatic Botany, 89(3), 303-310. doi:10.1016/j.aquabot.2008.03.004Peng, S.-H., Wang, W.-X., Li, X., & Yen, Y.-F. (2004). Metal partitioning in river sediments measured by sequential extraction and biomimetic approaches. Chemosphere, 57(8), 839-851. doi:10.1016/j.chemosphere.2004.07.015Peris, E. 1999. “Caracterización de los materiales de fondo del lago de la Albufera evaluación del nivel de aterramiento y caracterización mineralógica de los materiales así como de la carga contaminante persistente residente en el lago”. Departamento de Ingeniería de la Construcción, Universidad Politécnica de Valencia.Public database of Condederación Hidrográfica del Júcar. 2011. Available at:http://www.chj.gob.es/Redesdecalidad/red_ica.aspxSpeelmans, M., Lock, K., Vanthuyne, D. R. J., Hendrickx, F., Du Laing, G., Tack, F. M. G., & Janssen, C. R. (2010). Hydrological regime and salinity alter the bioavailability of Cu and Zn in wetlands. Environmental Pollution, 158(5), 1870-1875. doi:10.1016/j.envpol.2009.10.040Técnica y and Proyectos S. A. (TYPSA). 2004. “Estudio para el desarrollo sostenible de l’ Albufera de Valencia”. Confederación Hidrográfica del Júcar, Ministerio de Medio Ambiente.UNE. 77322:2003—Calidad del suelo. Extracción de elementos traza solubles en agua regia (ISO 11466:1995) AENOR, Madrid, Spain. 2003U.S. EPA. 2005. “Procedures for the derivation of Equilibrium Partitioning Sediment Benchmarks (ESBs) for the protection of benthic organisms: Metal mixtures (Cadmium, Copper, Lead, Nickel, Silver and Zinc). EPA-600-R-02-011”. Washington, DC, USA: Office of Research and Development.Van Griethuysen, C., de Lange, H. J., van den Heuij, M., de Bies, S. C., Gillissen, F., & Koelmans, A. A. (2006). Temporal dynamics of AVS and SEM in sediment of shallow freshwater floodplain lakes. Applied Geochemistry, 21(4), 632-642. doi:10.1016/j.apgeochem.2005.12.010Zheng, L., Xu, X. Q., & Xie, P. (2004). Seasonal and Vertical Distributions of Acid Volatile Sulfide and Metal Bioavailability in a Shallow, Subtropical Lake in China. Bulletin of Environmental Contamination and Toxicology, 72(2), 326-334. doi:10.1007/s00128-003-9000-

Identification of a possible role of thymine DNA glycosylase (TDG) in epigenome maintenance

Thymine DNA glycosylase (TDG) was discovered as an enzyme capable of removing uracil (U) and thymine (T) from G/U and G/T mispairs, respectively. Owing to this ability, TDG was proposed to initiate restoration of C/G pairs at sites of cytosine or 5-methycytosine (5-meC) deamination. In addition to products of base deamination, the substrate spectrum of TDG covers a wide range of DNA base damages resulting from base oxidation and alkylation. TDG was also found to engage in physical and functional interactions with transcription factors, and more recent evidence supports additional interactions with the de novo DNA methyltransferases Dnmt3a and 3b in the context of gene transcription. Together with its biochemical properties, these observations suggest that TDG might be targeted to gene regulatory sequences as part of a macromolecular assembly to control their functional integrity. TDG may counteract the mutagenic effects of C and 5-meC deamination in CG-rich regions and/or be involved in the maintenance of CpG promoter methylation patterns. A tight regulation of CpG methylation at gene regulatory regions is critical for accurate gene expression, proper cellular differentiation and embryonic development. A somewhat surprising but in this context consistent finding was that, in contrast to other DNA glycosylases, TDG is essential for proper fetal development since a targeted knockout of the gene leads to embryonic lethality. To gain insights into the biological functions of TDG, we aimed to establish and apply biochemical fractionation procedures for high affinity purification and structural and functional characterization of TDG containing proteins complexes. The first part of the thesis was concerned with biochemical characterization of the protein interaction network of TDG in living mammalian cells. To this end, I applied different approaches allowing high affinity isolation of protein complexes from mammalian cells, such as the tandem affinity purification (TAP) method as well as immunoprecipitation of endogenous protein and of the TDGa isoform from TdgA overexpressing embryonic stem (ES) cells. These efforts, however, did not reveal any TDG interacting partners in subsequent mass spectrometry (MS) analyses. These results were surprising, as TDG was previously reported to interact with transcription factors and DNA methyltransferases. Remarkably, however, all previously identified protein interactors of TDG were discovered in screen with the respective partner proteins, and under conditions of simultaneous overexpression of both interacting proteins. The only proteins ever identified in screen with TDG were Sumo1 and Sumo3, which turned out to covalently modify the glycosylase. For this reason, we decided to pursue our search with classical cell fractionation experiments. We first did gel filtration experiments from total cell lysates and showed that TDG is indeed able to form distinct multiprotein complexes in undifferentiated mouse embryonic stem cells that may also contain the RNA helicase p68. Further subcellular fractionation experiments then revealed that TDG is present in all cell compartments, with a significant fraction of nuclear TDG being associated with chromatin, together with p68 and de novo DNA methyltransferases. Together with published findings, these results suggested that protein complexes containing TDG might act in a chromatin-associated context, at gene regulatory regions. The developmental phenotype of Tdg-/- knockout mice and the interactions of TDG with factors involved in developmental gene regulation (e.g. retinoic acid receptors RAR/RXR) implicate a function of TDG during early development and cell differentiation, at times governed by dynamic changes in gene expression, DNA methylation and histone modifications. Such changes have been studied using a well-established during in vitro differentiation of ES cells to lineage committed neuronal progenitors (NPs). We thus aimed to address the function of TDG as part of chromatin associated protein complexes during the process of retinoic acid induced differentiation of ES cells to NPs. In the second part of the thesis we made use of a this well-established in vitro differentiation system to examine the genome-wide localization of TDG to chromatin by TDG chromatin immunoprecipitation (ChIP) and to correlate TDG association to chromatin with gene expression and DNA methylation changes linked to cellular differentiation. TDG ChIP combined with high throughput sequencing showed that TDG associates with high preference to CpG islands in promoters of actively transcribed genes or genes poised for transcriptional activation. Such CpG rich sequences are normally unmethylated in mammalian genomes. Interestingly, we found TDG to localize to promoters of many genes controlling pluripotency (e.g. Oct4, Nanog) and developmental processes (e.g. Sfrp2, Tgfb2, Gata6), thus, supporting a function of TDG in cell differentiation and/or embryonic development. As different lines of circumstantial evidence have associated TDG with changes in CpG methylation following activation of hormone responsive gene promoters, we went on to further test genome-wide promoter methylation in Tdg+/- and Tdg-/- NPs making use of a combination of methylated DNA immunoprecipitation (MeDIP) and microarray technology. This showed that the loss of TDG does not affect global promoter DNA methylation. Nevertheless, there were a number of significant differences, suggesting that TDG might affect the CpG methylation pattern at some promoters. Also, owing to the limited resolution of the MeDIP method, however, we could not exclude an involvement of TDG in the control of DNA methylation of specific promoter CpGs. Additional bisulfite sequencing of promoters of TDG bound developmental genes (e.g. Sfrp2, Tgfb2) in NPs and differentiated mouse embryonic fibroblasts (MEFs) have indeed proved that loss of TDG affects local changes in DNA methylation at particular CpGs. Subsequent analysis of genome-wide gene expression profiles of ES cells and differentiated Tdg+/- and Tdg-/- NPs revealed that a limited number of genes (229) are differentially regulated in ES, whereas substantial differences in gene expression in were observed in NPs (1022 genes). This implicated a specific function of TDG in the regulation of cell differentiation triggered gene expression changes. Detailed analysis of the expression of the Pax6 gene, accurate regulation of which is essential for proper neuron development, showed that its promoter is bound by TDG and that its transcription is inappropriately regulated upon further differentiation of Tdg-/- NPs into the neuronal lineage. Whereas Tdg+/- NPs efficiently downregulated Pax6 (50x) and further differentiated into neuron-like cells, Tdg-/- NPs only partially downregulated Pax6 gene expression (6x) and underwent apoptosis at day 2 after plating in neuronal medium. This phenotype was complemented by expression of TDGa, clearly implicating TDG in the regulation of Pax6 expression during differentiation of ES cells to terminal neurons. We further observed misregulation of pluripotency genes (e.g. Oct4) regulated by TDG bound promoters during early differentiation of ES cells. In the absence of TDG, ES cells showed the tendency to enter spontaneous and/or RA induced differentiation, suggesting a role for TDG in the regulation of pluripotency. During RA induced differentiation we further observed the activation of the neuron specific gene Lrrtm2 exclusively in TDG proficient cells. In addition, ChIP experiments showed that transcription factors involved in the activation of the Lrrtm2 gene (e.g. COUP-TFI, RAR) are not recruited to the respective promoter in Tdg-/- cells, suggesting that TDG might act passively as a scaffold factor important for the recruitment of transcription factors to promoter regions. I set out to clarify the biological function of TDG by investigating its molecular interactions in mammalian cells. I found that TDG, as a DNA repair enzyme, associates tightly with chromatin, where it localizes with high preference to CpG island promoters of active genes and genes poised to be expressed. I also found that the loss of TDG causes misregulation of genes during cell differentiation and that this appears to be related to a function of TDG in establishing and/or maintaining CpG methylation pattern in gene regulatory sequences. These discoveries implicate a novel function of DNA repair, in the maintenance not only of the genome, but also the epigenome