An end-to-end software solution for the analysis of high-throughput single-cell migration data

The systematic study of single-cell migration requires the availability of software for assisting data inspection, quality control and analysis. This is especially important for high-throughput experiments, where multiple biological conditions are tested in parallel. Although the field of cell migration can count on different computational tools for cell segmentation and tracking, downstream data visualization, parameter extraction and statistical analysis are still left to the user and are currently not possible within a single tool. This article presents a completely new module for the open-source, cross-platform CellMissy software for cell migration data management. This module is the first tool to focus specifically on single-cell migration data downstream of image processing. It allows fast comparison across all tested conditions, providing automated data visualization, assisted data filtering and quality control, extraction of various commonly used cell migration parameters, and non-parametric statistical analysis. Importantly, the module enables parameters computation both at the trajectory-and at the step-level. Moreover, this single-cell analysis module is complemented by a new data import module that accommodates multiwell plate data obtained from high-throughput experiments, and is easily extensible through a plugin architecture. In conclusion, the end-to-end software solution presented here tackles a key bioinformatics challenge in the cell migration field, assisting researchers in their highthroughput data processing

Multi-Behavioral Endpoint Testing Of An 87-Chemical Compound Library In Freshwater Planarians

There is an increased recognition in the field of toxicology of the value of medium-to-high-throughput screening methods using in vitro and alternative animal models. We have previously introduced the asexual freshwater planarian Dugesia japonica as a new alternative animal model and proposed that it is particularly well-suited for the study of developmental neurotoxicology. In this paper, we discuss how we have expanded and automated our screening methodology to allow for fast screening of multiple behavioral endpoints, developmental toxicity, and mortality. Using an 87-compound library provided by the National Toxicology Program (NTP), consisting of known and suspected neurotoxicants, including drugs, flame retardants, industrial chemicals, polycyclic aromatic hydrocarbons (PAHs), pesticides and presumptive negative controls, we further evaluate the benefits and limitations of the system for medium-throughput screening, focusing on the technical aspects of the system. We show that, in the context of this library, planarians are the most sensitive to pesticides with 16/16 compounds causing toxicity and the least sensitive to PAHs, with only 5/17 causing toxicity. Furthermore, while none of the presumptive negative controls were bioactive in adult planarians, 2/5, acetaminophen and acetylsalicylic acid, were bioactive in regenerating worms. Notably, these compounds were previously reported as developmentally toxic in mammalian studies. Through parallel screening of adults and developing animals, planarians are thus a useful model to detect such developmental-specific effects, which was observed for 13 chemicals in this library. We use the data and experience gained from this screen to propose guidelines for best practices when using planarians for toxicology screens

Research of advanced techniques for X-ray detectors and telescopes with applications to rockets and the LAMAR facility

A program for the development of high throughput instrumentation for X-ray astronomy based upon focusing optics is being carried out by the Smithsonian Astrophysical Observatory. The instrumentation is applicable to investigations requiring large area focusing optics for direct imaging or dispersive spectroscopy. The long range goals of this program are the development of telescopes and gratings for future major X-ray astronomy facilities, including additions to the LAMAR OSS-2/SHEAL experiment after the initial flights. Tests of the devices and their more immediate utilization in scientific investigations can be carried out with SPARTAN payloads deployed and retrieved by the Space Shuttle. However, the present backlog of approved SPARTAN missions is longer than the three-year duration of the program described in this program. Laboratory studies and breadboarding of instrumentation are discussed

Assessing the performance of ultrafast vector flow imaging in the neonatal heart via multiphysics modeling and In vitro experiments

Ultrafast vector flow imaging would benefit newborn patients with congenital heart disorders, but still requires thorough validation before translation to clinical practice. This paper investigates 2-D speckle tracking (ST) of intraventricular blood flow in neonates when transmitting diverging waves at ultrafast frame rate. Computational and in vitro studies enabled us to quantify the performance and identify artifacts related to the flow and the imaging sequence. First, synthetic ultrasound images of a neonate's left ventricular flow pattern were obtained with the ultrasound simulator Field II by propagating point scatterers according to 3-D intraventricular flow fields obtained with computational fluid dynamics (CFD). Noncompounded diverging waves (opening angle of 60 degrees) were transmitted at a pulse repetition frequency of 9 kHz. ST of the B-mode data provided 2-D flow estimates at 180 Hz, which were compared with the CFD flow field. We demonstrated that the diastolic inflow jet showed a strong bias in the lateral velocity estimates at the edges of the jet, as confirmed by additional in vitro tests on a jet flow phantom. Furthermore, ST performance was highly dependent on the cardiac phase with low flows (< 5 cm/s), high spatial flow gradients, and out-of-plane flow as deteriorating factors. Despite the observed artifacts, a good overall performance of 2-D ST was obtained with a median magnitude underestimation and angular deviation of, respectively, 28% and 13.5 degrees during systole and 16% and 10.5 degrees during diastole

Growth and characterization of binary and pseudo-binary 3-5 compounds exhibiting non-linear optical behavior. Undergraduate research opportunities in microgravity science and technology

In line with the specified objectives, a Bridgman-type growth configuration in which unavoidable end effects - conventionally leading to growth interface relocation - are compensated by commensurate input-power changes is developed; the growth rate on a microscale is predictable and unaffected by changes in heat transfer conditions. To permit quantitative characterization of the growth furnace cavity (hot-zone), a 3-D thermal field mapping technique, based on the thermal image, is being tested for temperatures up to 1100 C. Computational NIR absorption analysis was modified to now permit characterization of semi-insulating single crystals. Work on growth and characterization of bismuth-silicate was initiated. Growth of BSO (B12SiO20) for seed material by the Czochralski technique is currently in progress. Undergraduate research currently in progress includes: ground based measurements of the wetting behavior (contact angles) of semiconductor melts on substrates consisting of potential confinement materials for solidification experiments in a reduced gravity environment. Hardware modifications required for execution of the wetting experiments in a KC-135 facility are developed

A Deep Learning Approach to Denoise Optical Coherence Tomography Images of the Optic Nerve Head

Purpose: To develop a deep learning approach to de-noise optical coherence tomography (OCT) B-scans of the optic nerve head (ONH). Methods: Volume scans consisting of 97 horizontal B-scans were acquired through the center of the ONH using a commercial OCT device (Spectralis) for both eyes of 20 subjects. For each eye, single-frame (without signal averaging), and multi-frame (75x signal averaging) volume scans were obtained. A custom deep learning network was then designed and trained with 2,328 "clean B-scans" (multi-frame B-scans), and their corresponding "noisy B-scans" (clean B-scans + gaussian noise) to de-noise the single-frame B-scans. The performance of the de-noising algorithm was assessed qualitatively, and quantitatively on 1,552 B-scans using the signal to noise ratio (SNR), contrast to noise ratio (CNR), and mean structural similarity index metrics (MSSIM). Results: The proposed algorithm successfully denoised unseen single-frame OCT B-scans. The denoised B-scans were qualitatively similar to their corresponding multi-frame B-scans, with enhanced visibility of the ONH tissues. The mean SNR increased from $4.02 \pm 0.68$ dB (single-frame) to $8.14 \pm 1.03$ dB (denoised). For all the ONH tissues, the mean CNR increased from $3.50 \pm 0.56$ (single-frame) to $7.63 \pm 1.81$ (denoised). The MSSIM increased from $0.13 \pm 0.02$ (single frame) to $0.65 \pm 0.03$ (denoised) when compared with the corresponding multi-frame B-scans. Conclusions: Our deep learning algorithm can denoise a single-frame OCT B-scan of the ONH in under 20 ms, thus offering a framework to obtain superior quality OCT B-scans with reduced scanning times and minimal patient discomfort

The design and evaluation of grazing incidence relay optics

X-ray astronomy, both solar and celestial, has many needs for high spatial resolution observations which have to be performed with electronic detectors. If the resolution is not to be detector limited, plate scales in excess of 25 microns arc/sec, corresponding to focal lengths greater than 5 m, are required. In situations where the physical size is restricted, the problem can be solved by the use of grazing incidence relay optics. A system was developed which employs externally polished hyperboloid-hyperboloid surfaces to be used in conjunction with a Wolter-Schwarzschild primary. The secondary is located in front of the primary focus and provides a magnification of 4, while the system has a plate scale of 28 microns arc/sec and a length of 1.9 m. The design, tolerance specification, fabrication and performance at visible and X-ray wavelengths of this optical system are described