Domain specific cues improve robustness of deep learning based segmentation of ct volumes

Machine Learning has considerably improved medical image analysis in the past years. Although data-driven approaches are intrinsically adaptive and thus, generic, they often do not perform the same way on data from different imaging modalities. In particular Computed tomography (CT) data poses many challenges to medical image segmentation based on convolutional neural networks (CNNs), mostly due to the broad dynamic range of intensities and the varying number of recorded slices of CT volumes. In this paper, we address these issues with a framework that combines domain-specific data preprocessing and augmentation with state-of-the-art CNN architectures. The focus is not limited to optimise the score, but also to stabilise the prediction performance since this is a mandatory requirement for use in automated and semi-automated workflows in the clinical environment. The framework is validated with an architecture comparison to show CNN architecture-independent effects of our framework functionality. We compare a modified U-Net and a modified Mixed-Scale Dense Network (MS-D Net) to compare dilated convolutions for parallel multi-scale processing to the U-Net approach based on traditional scaling operations. Finally, we propose an ensemble model combining the strengths of different individual methods. The framework performs well on a range of tasks such as liver and kidney segmentation, without significant differences in prediction performance on strongly differing volume sizes and varying slice thickness. Thus our framework is an essential step towards performing robust segmentation of unknown real-world samples

Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions

Motivation: Cell fate decisions have a strong stochastic component. The identification of the underlying mechanisms therefore requires a rigorous statistical analysis of large ensembles of single cells that were tracked and phenotyped over time. Results: We introduce a probabilistic framework for testing elementary hypotheses on dynamic cell behavior using time-lapse cell-imaging data. Factor graphs, probabilistic graphical models, are used to properly account for cell lineage and cell phenotype information. Our model is applied to time-lapse movies of murine granulocyte-macrophage progenitor (GMP) cells. It decides between competing hypotheses on the mechanisms of their differentiation. Our results theoretically substantiate previous experimental observations that lineage instruction, not selection is the cause for the differentiation of GMP cells into mature monocytes or neutrophil granulocytes. Availability and implementation: The Matlab source code is available at http://treschgroup.de/Genealogies.html Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Beyond genealogies: Mutual information of causal paths to analyse single cell tracking data

Single cell tracking, based on the computerised analysis of time-lapse movies, is a sophisticated experimental technique to quantify single cell dynamics in time and space. Although the resulting cellular genealogies comprehensively describe the divisional history of each cell, there are many open questions regarding the statistical analysis of this type of data. In particular, it is unclear, how tracking uncertainties or spatial information of cellular development can correctly be incorporated into the analysis. Here we propose a generalised description of single cell tracking data by spatiotemporal networks that accounts for ambiguities in cell assignment as well as for spatial relations between cells. We present a way to measure correlations among cell states by analysing the mutual information in state space considering causal (time-respecting) paths and illustrate our approach by a corresponding example. We conclude that a comprehensive spatiotemporal description of single cell tracking data is ultimately necessary to fully exploit the information obtained by time-lapse imaging. Index Terms — cell tracking, lineage trees, temporal networks, information theory, stem cells 1

Involvement of GPR17 in Neuronal Fibre Outgrowth

Characterization of new pharmacological targets is a promising approach in research of neurorepair mechanisms. The G protein-coupled receptor 17 (GPR17) has recently been proposed as an interesting pharmacological target, e.g., in neuroregenerative processes. Using the well-established ex vivo model of organotypic slice co-cultures of the mesocortical dopaminergic system (prefrontal cortex (PFC) and substantia nigra/ventral tegmental area (SN/VTA) complex), the influence of GPR17 ligands on neurite outgrowth from SN/VTA to the PFC was investigated. The growthpromoting effects of Montelukast (MTK; GPR17- and cysteinyl-leukotriene receptor antagonist), the glial cell line-derived neurotrophic factor (GDNF) and of two potent, selective GPR17 agonists (PSB-16484 and PSB-16282) were characterized. Treatment with MTK resulted in a significant increase in mean neurite density, comparable with the effects of GDNF. The combination of MTK and GPR17 agonist PSB-16484 significantly inhibited neuronal growth. qPCR studies revealed an MTK-induced elevated mRNA-expression of genes relevant for neuronal growth. Immunofluorescence labelling showed a marked expression of GPR17 on NG2-positive glia. Western blot and RT-qPCR analysis of untreated cultures suggest a time-dependent, injury-induced stimulation of GPR17. In conclusion, MTK was identified as a stimulator of neurite fibre outgrowth, mediating its effects through GPR17, highlighting GPR17 as an interesting therapeutic target in neuronal regeneration

Enhancing the Thermal Performance of Slender Packed Beds through Internal Heat Fins

Slender packed beds are widely used in the chemical and process industry for heterogeneous catalytic reactions in tube-bundle reactors. Under safety and reaction engineering aspects, good radial heat transfer is of outstanding importance. However, because of local wall effects, the radial heat transport in the vicinity of the reactor wall is hindered. Particle-resolved computational fluid dynamics (CFD) is used to investigate the impact of internal heat fins on the near wall radial heat transport in slender packed beds filled with spherical particles. The simulation results are validated against experimental measurements in terms of particle count and pressure drop. The simulation results show that internal heat fins increase the conductive portion of the radial heat transport close to the reactor wall, leading to an overall increased thermal performance of the system. In a wide flow range (100<Rep<1000), an increase of up to 35% in wall heat transfer coefficient and almost 90% in effective radial thermal conductivity is observed, respectively

Enhancing the Thermal Performance of Slender Packed Beds through Internal Heat Fins

Slender packed beds are widely used in the chemical and process industry for heterogeneous catalytic reactions in tube-bundle reactors. Under safety and reaction engineering aspects, good radial heat transfer is of outstanding importance. However, because of local wall effects, the radial heat transport in the vicinity of the reactor wall is hindered. Particle-resolved computational fluid dynamics (CFD) is used to investigate the impact of internal heat fins on the near wall radial heat transport in slender packed beds filled with spherical particles. The simulation results are validated against experimental measurements in terms of particle count and pressure drop. The simulation results show that internal heat fins increase the conductive portion of the radial heat transport close to the reactor wall, leading to an overall increased thermal performance of the system. In a wide flow range (100<Rep<1000), an increase of up to 35% in wall heat transfer coefficient and almost 90% in effective radial thermal conductivity is observed, respectively.TU Berlin, Open-Access-Mittel – 202

Cell-accurate optical mapping across the entire developing heart

Organogenesis depends on orchestrated interactions between individual cells and morphogenetically relevant cues at the tissue level. This is true for the heart, whose function critically relies on well-ordered communication between neighboring cells, which is established and fine-tuned during embryonic development. For an integrated understanding of the development of structure and function, we need to move from isolated snap-shot observations of either microscopic or macroscopic parameters to simultaneous and, ideally continuous, cell-to-organ scale imaging. We introduce cell-accurate three-dimensional Ca2+-mapping of all cells in the entire electro-mechanically uncoupled heart during the looping stage of live embryonic zebrafish, using high-speed light sheet microscopy and tailored image processing and analysis. We show how myocardial region-specific heterogeneity in cell function emerges during early development and how structural patterning goes hand-in-hand with functional maturation of the entire heart. Our method opens the way to systematic, scale-bridging, in vivo studies of vertebrate organogenesis by cell-accurate structure-function mapping across entire organs