Automated Reconstruction of Dendritic and Axonal Trees by Global Optimization with Geometric Priors

We present a novel probabilistic approach to fully automated delineation of tree structures in noisy 2D images and 3D image stacks. Unlike earlier methods that rely mostly on local evidence, ours builds a set of candidate trees over many different subsets of points likely to belong to the optimal tree and then chooses the best one according to a global objective function that combines image evidence with geometric priors. Since the best tree does not necessarily span all the points, the algorithm is able to eliminate false detections while retaining the correct tree topology. Manually annotated brightfield micrographs, retinal scans and the DIADEM challenge datasets are used to evaluate the performance of our method. We used the DIADEM metric to quantitatively evaluate the topological accuracy of the reconstructions and showed that the use of the geometric regularization yields a substantial improvemen

Phylogenetic signal in phonotactics

Phylogenetic methods have broad potential in linguistics beyond tree inference. Here, we show how a phylogenetic approach opens the possibility of gaining historical insights from entirely new kinds of linguistic data – in this instance, statistical phonotactics. We extract phonotactic data from 112 Pama-Nyungan vocabularies and apply tests for phylogenetic signal, quantifying the degree to which the data reflect phylogenetic history. We test three datasets: (1) binary variables recording the presence or absence of biphones (two-segment sequences) in a lexicon (2) frequencies of transitions between segments, and (3) frequencies of transitions between natural sound classes. Australian languages have been characterized as having a high degree of phonotactic homogeneity. Nevertheless, we detect phylogenetic signal in all datasets. Phylogenetic signal is greater in finer-grained frequency data than in binary data, and greatest in natural-class-based data. These results demonstrate the viability of employing a new source of readily extractable data in historical and comparative linguistics.1. Introduction 1.1 Motivations 1.2 Phonotactics as a source of historical signal 2. Phylogenetic signal 3. Materials 3.1 Language sample 3.2 Wordlists 3.3 Reference phylogeny 4. Phylogenetic signal in binary phonotactic data 4.1 Results for binary phonotactic data 4.2 Robustness checks 5. Phylogenetic signal in continuous phonotactic data 5.1 Robustness checks 5.2 Forward transitions versus backward transitions 5.3 Normalization of character values 6. Phylogenetic signal in natural-class-based characters 6.1 Natural-class-based characters versus biphones 7. Discussion 7.1 Overall robustness 7.2 Limitations 8. Conclusio

Hillview:A trillion-cell spreadsheet for big data

Hillview is a distributed spreadsheet for browsing very large datasets that cannot be handled by a single machine. As a spreadsheet, Hillview provides a high degree of interactivity that permits data analysts to explore information quickly along many dimensions while switching visualizations on a whim. To provide the required responsiveness, Hillview introduces visualization sketches, or vizketches, as a simple idea to produce compact data visualizations. Vizketches combine algorithmic techniques for data summarization with computer graphics principles for efficient rendering. While simple, vizketches are effective at scaling the spreadsheet by parallelizing computation, reducing communication, providing progressive visualizations, and offering precise accuracy guarantees. Using Hillview running on eight servers, we can navigate and visualize datasets of tens of billions of rows and trillions of cells, much beyond the published capabilities of competing systems