Showing papers by "Olaf Ronneberger published in 2017"

An objective comparison of cell-tracking algorithms

Abstract: We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge.

A new fate mapping system reveals context-dependent random or clonal expansion of microglia

Abstract: Microglia constitute a highly specialized network of tissue-resident immune cells that is important for the control of tissue homeostasis and the resolution of diseases of the CNS. Little is known about how their spatial distribution is established and maintained in vivo. Here we establish a new multicolor fluorescence fate mapping system to monitor microglial dynamics during steady state and disease. Our findings suggest that microglia establish a dense network with regional differences, and the high regional turnover rates found challenge the universal concept of microglial longevity. Microglial self-renewal under steady state conditions constitutes a stochastic process. During pathology this randomness shifts to selected clonal microglial expansion. In the resolution phase, excess disease-associated microglia are removed by a dual mechanism of cell egress and apoptosis to re-establish the stable microglial network. This study unravels the dynamic yet discrete self-organization of mature microglia in the healthy and diseased CNS.

Invited Talk: U-Net Convolutional Networks for Biomedical Image Segmentation

Abstract: In the last years, deep convolutional networks have outperformed the state of the art in many visual recognition tasks. A central challenge for its wide adoption in the bio-medical imaging field is the limited amount of annotated training images. In this talk, I will present our u-net for biomedical image segmentation. The architecture consists of an analysis path and a synthesis path with additional shortcut-connections.

A 3D digital atlas of the Nicotiana tabacum root tip and its use to investigate changes in the root apical meristem induced by the Agrobacterium 6b oncogene.

Abstract: Summary Using the intrinsic Root Coordinate System (iRoCS) Toolbox, a digital atlas at cellular resolution has been constructed for Nicotiana tabacum roots. Mitotic cells and cells labeled for DNA replication with 5-ethynyl-2’-deoxyuridine (EdU) were mapped. The results demonstrate that iRoCS analysis can be applied to thicker roots than those of Arabidopsis thaliana without histological sectioning. A three-dimensional (3-D) analysis of the root tip showed that tobacco roots undergo several irregular periclinal and tangential divisions. Irrespective of cell type, rapid cell elongation starts at the same distance from the quiescent center, however, boundaries between cell proliferation and transition domains are cell-type specific. The data support the existence of a transition domain in tobacco roots. Cell endoreduplication starts in the transition domain and continues into the elongation zone. The tobacco root map was subsequently used to analyze root organization changes caused by inducible expression of the Agrobacterium 6b oncogene. In tobacco roots expressing the 6b gene, the root apical meristem was shorter and radial cell growth was reduced, but the mitotic and DNA replication indexes were not affected. The epidermis of 6b-expressing roots produced less files and underwent abnormal periclinal divisions. The periclinal division leading to mature endodermis and cortex3 cell files was delayed. These findings define additional targets for future studies on the mode of action of the Agrobacterium 6b oncogene. This article is protected by copyright. All rights reserved.

Spatiotemporal Deformable Prototypes for Motion Anomaly Detection

Abstract: This paper presents an approach for motion-based anomaly detection, where a prototype pattern is detected and elastically registered against a test sample to detect anomalies in the test sample. The prototype model is learned from multiple sequences to define accepted variations. "Supertrajectories" based on hierarchical clustering of dense point trajectories serve as an efficient and robust representation of motion patterns. An efficient hashing approach provides transformation hypotheses that are refined by a spatiotemporal elastic registration. We propose a new method for elastic registration of 3D+time trajectory patterns that induces spatial elasticity from trajectory affinities. The method is evaluated on a new motion anomaly dataset of juggling patterns and performs well in detecting subtle anomalies. Moreover, we demonstrate the applicability to biological motion patterns.