Kleinvoet: a Spatially-Distributed Temporally-Synchronised Infrasonic Recorder

We present the hardware design of a high-fidelity, low-cost infrasonic-capable (6 Hz) passive acoustic monitoring (PAM) prototype instrument. The device allows temporal synchronisation using a variety of global navigation satellite system (GNSS) constellations. This allows the recordings made by independent spatially-distributed nodes to be synchronised in time for acoustic monitoring and localisation using, for example, time difference of arrival (TDOA). Each node is capable of sampling at 24-bit resolution with a sampling frequency that is adjustable between 8 kHz and 192 kHz. Audio samples are stored locally on a microSD card, along with timestamp and location metadata

Educated mother-tongue South African English: A corpus approach

South Africa is anecdotally known for its complex system of speech varieties correlating with variables such as ethnicity, first language, class and education. These intuitions (e.g. Lass 1990) require further investigation, especially in the context of a changing South Africa where language variety plays a key role in identifying social, economic and ethnic group membership. Thus, in this research, the extent to which these variables play a role in variety is explored using a corpus approach (the nature of class and race in the corpus is discussed more fully later in the article). The corpus project, focusing primarily on accent, has been undertaken by members of the Department of English Language and Linguistics at Rhodes University in South Africa, collaborating with staff from the Department of Electrical and Electronic Engineering from Stellenbosch University, South Africa. A corpus (the first of its kind) is being compiled, comprising the speech of educated, white, mother-tongue speakers of South African English (as distinct from Afrikaans English, Indian English, and the second language (L2) varieties of English used by speakers of indigenous African languages), and data collection is well under way. This short article aims to describe the aims of the project, and the methodological approach which underpins it, as well as to highlight some of the more problematic aspects of the research

Time-optimal control by means of neural networks

Thesis (M. Ing.) -- University of Stellenbosch, 1993.One copy microfiche.Full text to be digitised and attached to bibliographic record

The impact of accent identification errors on speech recognition of South African English

For successful deployment, a South African English speech recognition system must be capable of processing the prevalent accents in this variety of English. Previous work dealing with the different accents of South African English has considered the case in which the accent of the input speech is known. Here we focus on the practical scenario in which the accent of the input speech is unknown and accent identification must occur at recognition time. By means of a set of contrastive experiments, we determine the effect which errors in the identification of the accent have on speech recognition performance. We focus on the specific configuration in which a set of accent-specific speech recognisers operate in parallel, thereby delivering both a recognition hypothesis as well as an identified accent in a single step. We find that, despite their considerable number, the accent identification errors do not lead to degraded speech recognition performance. We conclude that, for our South African English data, there is no benefit of including a more complex explicit accent identification component in the overall speech recognition system

Regression adjusted colocalisation colour mapping (RACC): A novel biological visual analysis method for qualitative colocalisation analysis of 3D fluorescence micrographs.

The qualitative analysis of colocalisation in fluorescence microscopy is of critical importance to the understanding of biological processes and cellular function. However, the degree of accuracy achieved may differ substantially when executing different yet commonly utilized colocalisation analyses. We propose a novel biological visual analysis method that determines the correlation within the fluorescence intensities and subsequently uses this correlation to assign a colourmap value to each voxel in a three-dimensional sample while also highlighting volumes with greater combined fluorescence intensity. This addresses the ambiguity and variability which can be introduced into the visualisation of the spatial distribution of correlation between two fluorescence channels when the colocalisation between these channels is not considered. Most currently employed and generally accepted methods of visualising colocalisation using a colourmap can be negatively affected by this ambiguity, for example by incorrectly indicating non-colocalised voxels as positively correlated. In this paper we evaluate the proposed method by applying it to both synthetic data and biological fluorescence micrographs and demonstrate how it can enhance the visualisation in a robust way by visualising only truly colocalised regions using a colourmap to indicate the qualitative measure of the correlation between the fluorescence intensities. This approach may substantially support fluorescence microscopy applications in which precise colocalisation analysis is of particular relevance

Virtual reality assisted microscopy data visualization and colocalization analysis

CITATION: Theart, R. P., Loos, B. & Niesler, T. R. 2016. Virtual reality assisted microscopy data visualization and colocalization analysis. BMC Bioinformatics, 18(2):64, doi:10.1186/s12859-016-1446-2.The original publication is available at https://bmcbioinformatics.biomedcentral.comBackground: Confocal microscopes deliver detailed three-dimensional data and are instrumental in biological analysis and research. Usually, this three-dimensional data is rendered as a projection onto a two-dimensional display. We describe a system for rendering such data using a modern virtual reality (VR) headset. Sample manipulation is possible by fully-immersive hand-tracking and also by means of a conventional gamepad. We apply this system to the specific task of colocalization analysis, an important analysis tool in biological microscopy. We evaluate our system by means of a set of user trials. Results: The user trials show that, despite inaccuracies which still plague the hand tracking, this is the most productive and intuitive interface. The inaccuracies nevertheless lead to a perception among users that productivity is low, resulting in a subjective preference for the gamepad. Fully-immersive manipulation was shown to be particularly effective when defining a region of interest (ROI) for colocalization analysis. Conclusions: Virtual reality offers an attractive and powerful means of visualization for microscopy data. Fully immersive interfaces using hand tracking show the highest levels of intuitiveness and consequent productivity. However, current inaccuracies in hand tracking performance still lead to a disproportionately critical user perception.https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1446-2Publisher's versio

Computer simulation and physical phantom models for estimating the dielectric properties of rhinoceros tissue.

In vivo and ex vivo sensors have the potential to aid tracking and anti-poaching endeavours and provide new insights into rhinoceros physiology and environment. However, the propagation of electromagnetic signals in rhinoceros tissue is currently not known. We present simulation and agar models of the rhinoceros that allow the investigation of electromagnetic propagation by in vivo and ex vivo devices without the need for surgery. Since the dielectric properties of rhinoceros tissue have not been documented, the conductivity and permittivity of the skin, fat, muscle, blood and other organs are first approximated by means of a meta-analysis that includes animals with similar physical properties. Subsequently, we develop anatomical models that include dermal layers, internal organs and a skeleton. We also develop a flank model that serves as an approximation of the anatomical model in certain situations. These models are used to determine the viability of communication between an in vivo device and an ex vivo device attached to the hind leg of the animal. Two types of antenna (microstrip-fed planar elliptical monopole antenna and printed inverted-F antenna) and three feasible implant locations (back, neck and chest) are considered. In addition to the computer models, phantom recipes using salt, sugar and agar are developed to match the dielectric properties of each tissue type at the industrial, scientific and medical (ISM) frequencies of 403MHz, 910MHz and 2.4GHz. The average error between the measured and theoretically predicted dielectric values was 6.22% over all recipes and 4.49% for the 2.4 GHz recipe specifically. When considering the predicted efficiency of the transmitting and receiving antennas, an agreement of 67.38% was demonstrated between the computer simulations and laboratory measurements using the agar rhinoceros flank models. Computer simulations using the anatomical model of the rhinoceros indicate that the chest is the optimal implant location and that best signal propagation is achieved using the planar inverted-F antenna (PIFA). Using this configuration, the simulations indicate that communication between the implant and an ex vivo device attached to the hind leg is challenging but possible. Furthermore, we find that the inclusion of factors such as the density and temperature of the phantom materials were found to be critical to the achievement of good agreement between practice and simulation

Improved region of interest selection and colocalization analysis in three-dimensional fluorescence microscopy samples using virtual reality.

Although modern fluorescence microscopy produces detailed three-dimensional (3D) datasets, colocalization analysis and region of interest (ROI) selection is most commonly performed two-dimensionally (2D) using maximum intensity projections (MIP). However, these 2D projections exclude much of the available data. Furthermore, 2D ROI selections cannot adequately select complex 3D structures which may inadvertently lead to either the exclusion of relevant or the inclusion of irrelevant data points, consequently affecting the accuracy of the colocalization analysis. Using a virtual reality (VR) enabled system, we demonstrate that 3D visualization, sample interrogation and analysis can be achieved in a highly controlled and precise manner. We calculate several key colocalization metrics using both 2D and 3D derived super-resolved structured illumination-based data sets. Using a neuronal injury model, we investigate the change in colocalization between Tau and acetylated α-tubulin at control conditions, after 6 hours and again after 24 hours. We demonstrate that performing colocalization analysis in 3D enhances its sensitivity, leading to a greater number of statistically significant differences than could be established when using 2D methods. Moreover, by carefully delimiting the 3D structures under analysis using the 3D VR system, we were able to reveal a time dependent loss in colocalization between the Tau and microtubule network as an early event in neuronal injury. This behavior could not be reliably detected using a 2D based projection. We conclude that, using 3D colocalization analysis, biologically relevant samples can be interrogated and assessed with greater precision, thereby better exploiting the potential of fluorescence-based image analysis in biomedical research

Mitochondrial event localiser (MEL) to quantitativelydescribe fission, fusion and depolarisation in the three-dimensional space

CITATION: Theart, R. P., et al. 2020. Mitochondrial event localiser (MEL) to quantitativelydescribe fission, fusion and depolarisation in the three-dimensional space. PLoS ONE, 15(12): e0229634, doi:10.1371/journal.pone.0229634The original publication is available at https://journals.plos.org/plosone/Publication of this article was funded by the Stellenbosch University Open Access FundENGLISH ABSTRACT: Mitochondrial fission and fusion play an important role not only in maintaining mitochondrial homeostasis but also in preserving overall cellular viability. However, quantitative analysis based on the three-dimensional localisation of these highly dynamic mitochondrial events in the cellular context has not yet been accomplished. Moreover, it remains largely uncertain where in the mitochondrial network depolarisation is most likely to occur. We present the mitochondrial event localiser (MEL), a method that allows high-throughput, automated and deterministic localisation and quantification of mitochondrial fission, fusion and depolarisation events in large three-dimensional microscopy time-lapse sequences. In addition, MEL calculates the number of mitochondrial structures as well as their combined and average volume for each image frame in the time-lapse sequence. The mitochondrial event locations can subsequently be visualised by superposition over the fluorescence micrograph z-stack. We apply MEL to both control samples as well as to cells before and after treatment with hydrogen peroxide (H2O2). An average of 9.3/7.2/2.3 fusion/fission/depolarisation events per cell were observed respectively for every 10 sec in the control cells. With peroxide treatment, the rate initially shifted toward fusion with and average of 15/6/3 events per cell, before returning to a new equilibrium not far from that of the control cells, with an average of 6.2/6.4/3.4 events per cell. These MEL results indicate that both pre-treatment and control cells maintain a fission/fusion equilibrium, and that depolarisation is higher in the post-treatment cells. When individually validating mitochondrial events detected with MEL, for a representative cell for the control and treated samples, the true-positive events were 47%/49%/14% respectively for fusion/fission/depolarisation events. We conclude that MEL is a viable method of quantitative mitochondrial event analysis.https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229634Publishers' Versio