An automated workflow for parallel processing of large multiview SPIM recordings

Multiview light sheet fluorescence microscopy (LSFM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance cluster (HPC). Here we introduce an automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse LSFM data on a single workstation or in parallel on a HPC. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing LSFM data in a fraction of the time required to collect it.Comment: 13 pages with supplement, LATEX; 1 table, 1 figure, 2 supplementary figures, 2 supplementary lists, 2 supplementary tables; corrected error in results table, results unchange

A Primal-Dual Solver for Large-Scale Tracking-by-Assignment

We propose a fast approximate solver for the combinatorial problem known as tracking-by-assignment, which we apply to cell tracking. The latter plays a key role in discovery in many life sciences, especially in cell and developmental biology. So far, in the most general setting this problem was addressed by off-the-shelf solvers like Gurobi, whose run time and memory requirements rapidly grow with the size of the input. In contrast, for our method this growth is nearly linear. Our contribution consists of a new (1) decomposable compact representation of the problem; (2) dual block-coordinate ascent method for optimizing the decomposition-based dual; and (3) primal heuristics that reconstructs a feasible integer solution based on the dual information. Compared to solving the problem with Gurobi, we observe an up to~60~times speed-up, while reducing the memory footprint significantly. We demonstrate the efficacy of our method on real-world tracking problems.Comment: 23rd International Conference on Artificial Intelligence and Statistics (AISTATS), 202

scenery: Flexible Virtual Reality Visualization on the Java VM

Life science today involves computational analysis of a large amount and variety of data, such as volumetric data acquired by state-of-the-art microscopes, or mesh data from analysis of such data or simulations. Visualization is often the first step in making sense of data, and a crucial part of building and debugging analysis pipelines. It is therefore important that visualizations can be quickly prototyped, as well as developed or embedded into full applications. In order to better judge spatiotemporal relationships, immersive hardware, such as Virtual or Augmented Reality (VR/AR) headsets and associated controllers are becoming invaluable tools. In this work we introduce scenery, a flexible VR/AR visualization framework for the Java VM that can handle mesh and large volumetric data, containing multiple views, timepoints, and color channels. scenery is free and open-source software, works on all major platforms, and uses the Vulkan or OpenGL rendering APIs. We introduce scenery's main features and example applications, such as its use in VR for microscopy, in the biomedical image analysis software Fiji, or for visualizing agent-based simulations.Comment: Added IEEE DOI, version published at VIS 201

Auf dem Weg zum nachhaltigen Stadtviertel

Wie die nachhaltige Stadt der Zukunft aussehen könnte, zeigt der Stadtteil „Scharnhauser Park“ in Ostfildern bei Stuttgart. In diesem Quartier versuchen Wissenschaftler und Investoren, einen ganzen Stadtteil so optimal wie möglich nach nachhaltigen Gesichtspunkten zu gestalten

Increased cancer prevalence in peripartum cardiomyopathy

Objectives This study was designed to analyze the prevalence and potential genetic basis of cancer and heart failure in peripartum cardiomyopathy (PPCM). Background PPCM manifests as heart failure late in pregnancy or postpartum in women without previous heart disease. Methods Clinical history and cancer prevalence were evaluated in a cohort of 236 PPCM patients from Germany and Sweden. Exome sequencing assessed variants in 133 genes associated with cancer predisposition syndromes (CPS) and in 115 genes associated with dilated/hypertrophic cardiomyopathy (DCM/HCM) in 14 PPCM patients with a history of cancer, and in 6 PPCM patients without a history of cancer. Results The prevalence of cancer was 16-fold higher (8.9%, 21 of 236 patients) in PPCM patients compared to age-matched women (German cancer registry, Robert-Koch-Institute: 0.59%; p < 0.001). Cancer before PPCM occurred in 12 of 21 patients of whom 11 obtained cardiotoxic cancer therapies. Of those, 17% fully recovered cardiac function by 7 ± 2 months of follow-up compared to 55% of PPCM patients without cancer (p = 0.015). Cancer occurred after PPCM in 10 of 21 patients; 80% had left ventricular ejection fraction of ≥50% after cancer therapy. Whole-exome sequencing in 14 PPCM patients with cancer revealed that 43% (6 of 14 patients) carried likely pathogenic (Class IV) or pathogenic (Class V) gene variants associated with DCM/HCM in CPT2, DSP, MYH7, TTN, and/or with CPS in ATM, ERCC5, NBN, RECQL4, and SLX4. All CPS variants affected DNA damage response genes. Conclusions Cardiotoxic cancer therapy before PPCM is associated with delayed full recovery. The high cancer prevalence in PPCM is linked to likely pathogenic/pathogenic gene variants associated with DCM/HCM and/or CPS/DNA damage response–related cancer risk. This may warrant genetic testing and screening for heart failure in pregnant women with a cancer history and screening for cancer in PPCM patients

The association between frailty and MRI features of cerebral small vessel disease

Abstract: Frailty is a common syndrome in older individuals that is associated with poor cognitive outcome. The underlying brain correlates of frailty are unclear. The aim of this study was to investigate the association between frailty and MRI features of cerebral small vessel disease in a group of non-demented older individuals. We included 170 participants who were classified as frail (n = 30), pre-frail (n = 85) or non-frail (n = 55). The association of frailty and white matter hyperintensity volume and shape features, lacunar infarcts and cerebral perfusion was investigated by regression analyses adjusted for age and sex. Frail and pre-frail participants were older, more often female and showed higher white matter hyperintensity volume (0.69 [95%-CI 0.08 to 1.31], p = 0.03 respectively 0.43 [95%-CI: 0.04 to 0.82], p = 0.03) compared to non-frail participants. Frail participants showed a non-significant trend, and pre-frail participants showed a more complex shape of white matter hyperintensities (concavity index: 0.04 [95%-CI: 0.03 to 0.08], p = 0.03; fractal dimensions: 0.07 [95%-CI: 0.00 to 0.15], p = 0.05) compared to non-frail participants. No between group differences were found in gray matter perfusion or in the presence of lacunar infarcts. In conclusion, increased white matter hyperintensity volume and a more complex white matter hyperintensity shape may be structural brain correlates of the frailty phenotype

Probing the Hofmeister Effect with Ultrafast Core Hole Spectroscopy

In the current work, X-ray emission spectra of aqueous solutions of different inorganic salts within the Hofmeister series are presented. The results reflect the direct interaction of the ions with the water molecules and therefore, reveal general properties of the salt-water interactions. Within the experimental precision a significant effect of the ions on the water structure has been observed but no ordering according to the structure maker/structure breaker concept could be mirrored in the results indicating that the Hofmeister effect-if existent-may be caused by more complex interactions