Creating a platform for the democratisation of Deep Learning in microscopy

One of the major technological success stories of the last decade has been the advent of deep learning (DL), which has touched almost every aspect of modern life after a breakthrough performance in an image detection challenge in 2012. The bioimaging community quickly recognised the prospect of the automated ability to make sense of image data with near-human performance as potentially ground-breaking. In the decade since, hundreds of publications have used this technology to tackle many problems related to image analysis, such as labelling or counting cells, identifying cells or organelles of interest in large image datasets, or removing noise or improving the resolution of images. However, the adoption of DL tools in large parts of the bioimaging community has been slow, and many tools have remained in the hands of developers. In this project, I have identified key barriers which have prevented many bioimage analysts and microscopists from accessing existing DL technology in their field and have, in collaboration with colleagues, developed the ZeroCostDL4Mic platform, which aims to address these barriers. This project is inspired by the observation that the most significant impact technology can have in science is when it becomes ubiquitous, that is, when its use becomes essential to address the community’s questions. This work represents one of the first attempts to make DL tools accessible in a transparent, code-free, and affordable manner for bioimage analysis to unlock the full potential of DL via its democratisation for the bioimaging community

Composite carbon membranes for the desalination of water

Thesis (MSc (Chemistry and Polymer Science))--University of Stellenbosch, 2007.Electrodialysis is a method of water desalination which involves the separation of TDS through an ion-exchange membrane under a potential gradient. In this study it was attempted to reverse engineer the composite carbon ion-exchange membrane used in a prototype plant and electrochemically evaluate a prototype desalination cell. The influence of applied potential on the capacitance of the various electrode surfaces and possible electrode reactions was investigated. A model was also suggested to describe the conductivity through the membrane. The composition of composite carbon membranes were determined by compositional analysis using various analytical tools. Elemental analysis, done with PIXE and EDS, showed that the membranes contained chloride, fluoride, oxygen, carbon, and possibly hydrogen. With LC-MS and IR it was established that the membranes consisted of two polymers with no carbonyl or aromatic functional groups. After further thermal analysis the following possible compounds remained: hexafluoropropylene tetrafluoroethylene copolymer, polychlorotrifluoroethylene (PCTFE), polyoxyethylene oxide (PEO) and polyethylene glycol (PEG). This assessment is in good agreement with the contents of US patent 4,153, 661, which describes the composite membrane

Aspekt und Grad

Der chinesische Grammatiker Guō Ruì (1991) erarbeitet sich die Tempusklassen des Hàn-Chinesischen, die in Anhang A vorgestellt werden. Dabei beschäftigt er sich auch mit der Tempussemantik des Verbalaspekts 了(-le) und der Finalpartikel了(-le). Guō Ruì (1997) räumt den Aspektbedeutungen der Verbform innerhalb dieses Tempus-Systems eine zentrale Stellung ein, ebenso der Existenz-negation 没有(méiyou) nicht haben und ihrem Gegenstück, dem Negationswort不(bù). Mǎ Qìngzhū (1998) befasst sich u.a. auch mit der Gradsemantik der Finalpartikel了(-le). An der Finalpartikel ist eine ähnliche Verflechtung von Aspekt- und Gradsemantik zu beobachten, wie am Aspekt- und Gradadverb schon im Deutschen. Er zeigt, wie die Finalpartikel die Interpretation der mehrdeutigen Temporalangabe, die Guō Ruì (1991) in seine Untersu-chung mit aufgenommen hat, beeinflusst. Mit der vorliegenden Arbeit sollen die Grundlagen für eine Anbindung an die Untersuchungen von Bertinetto und Delfitto (2000) geschaffen werden. Zu dem Zweck werden die Beschreibungen, die Guō Ruì (1991) von der Bedeutung der chinesischen Verbformen gibt, in die Tempuskategorien übersetzt (zum Teil in Anlehnung an Carlota Smith 1993). Frucht dieser Bemühungen sind zwei Tabellen: Tabelle 2 (Kap. 1, aspektuelle und zeitreferentielle Ambiguität des Verbalaspekts了(-le)) und Tabelle 3 (Kap. 6, das aktionelle und aspektuelle Milieu, in dem die Interpretation der ambigen Zeitspannen-Temporalangabe festgelegt wird, Hypothese)

The importance of organic detritus in lotic ecosystems: Aspects of trophic interactions

Very little research has been carried out on detrital energetics and pathways in lotic ecosystems. Most investigations have concentrated on the degradation of allochthonous plant litter by fungi, with a glance at heterotrophic bacteria associated with decaying litter. In this short review, the author describes what is known of the detrition of plant litter in lotic waters, which results from the degradative activities of colonising saprophytic fungi and bacteria, and goes on to relate this process to those invertebrates that consume coarse and/or fine particulate detritus, or dissolved organic matter that aggregates into colloidal exopolymer particles. It is clear that many of the key processes involved in the relationships between the physical, chemical, biotic and biochemical elements present in running waters are very complex and poorly understood. Those few aspects for which there are reliable models with predictive power have resulted from data collections made over periods of 20 years or more. Comprehensive research of single catchments would provide a fine opportunity to collect data over a long period

Seasonal variations of water and sediment quality parameters in endorheic reed pans on the Mpumalanga Highveld

The Mpumalanga Lakes District consists of approximately 320 pans, of which less than 3% are classified as reed pans. There is limited information available on reed pans and as a result they are at risk of various anthropogenic activities, for example mining and agriculture. Four reed pans were selected and assessed to determine seasonal trends of a variety of water and sediment quality parameters. The study took place over one seasonal cycle from 2008–2009; samples were collected seasonally to account for various hydrological extremes. Water samples were collected and their nutrient and chlorophyll a concentrations were determined, while various other water quality parameters were measured in situ. Sediment samples were analysed for physical and chemical properties, namely, grain size and organic carbon content. The seasonal changes in concentrations of As, Cr, Cu, Fe, Pb, Mn, Mo, Ni, Se, Sr, U and Zn were also analysed within the surface water and sediment. Increased nutrient concentrations within the water were evident during spring and summer at some of the sites, which influenced other water quality variables, e.g., dissolved oxygen and pH. Seasonal trends in metal concentrations were influenced by the prevailing environmental conditions (e.g., rainfall) experienced at the selected sites as well as physical and chemical properties (e.g., grain size and organic carbon content). This study showed distinct seasonal variability of water and sediment quality parameters in endorheic reed pans on the Mpumalanga Highveld. There is a need for further studies on all of the different types of pans in terms of their water and sediment quality. This type of information will allow for a sound and defensible scientific basis for the assessment of likely impacts (e.g., eutrophication), the evaluation of the significance of these impacts, and the design of remedial and preventative measures

M1/M2 Macrophage Polarity in Normal and Complicated Pregnancy

Tissue macrophages play an important role in all stages of pregnancy, including uterine stromal remodeling (decidualization) before embryo implantation, parturition, and postpartum uterine involution. The activation state and function of utero-placental macrophages are largely dependent on the local tissue microenvironment. Thus, macrophages are involved in a variety of activities such as regulation of immune cell activities, placental cell invasion, angiogenesis, and tissue remodeling. Disruption of the uterine microenvironment, particularly during the early stages of pregnancy (decidualization, implantation, and placentation) can have profound effects on macrophage activity and subsequently impact pregnancy outcome. In this review, we will provide an overview of the temporal and spatial regulation of utero-placental macrophage activation during normal pregnancy in humans and rodents with a focus on more recent findings. We will also discuss the role of M1/M2 dysregulation within the intrauterine environment during adverse pregnancy outcomes

The importance of organic detritus in lotic ecosystems: aspects of trophic interactions

Ecological studies on lotic systems pay some lip-service to the importance ofthe micro-biota and their function within ecosystems, but experience tells methat this dimension is usually ignored in grand research schemes. I hope tomake a convincing case for their inclusion in catchment ecosystem research.Others, more expert than I, will plead the importance of photosyntheticmicro-organisms. In this short review, "microbiological aspects" cover theprocessing of organic detritus in lotic waters by heterotrophic microorganisms

Spectroscopy, morphology, and electrochemistry of electrospun polyamic acid nanofibers

Polyamic acid (PAA) nanofibers produced by using the electrospinning method were fully characterized in terms of morphology and spectroscopy. A PAA nanofiber–modified screen-printed carbon electrode was applied to the detection of selected sulfonamides by following an electroanalytical protocol. The polyamic acid (PAA) nanofibers were characterized using Fourier transform infrared (FTIR) spectroscopy to study the integrity of polyamic acid functional groups as nanofibers by comparing them to chemically synthesized polyamic acid. A scanning electron microscope (SEM) was used to confirm the morphology of the produced nanofibers and 3D arrangement at the electrode interface. The Brunauer–Emmett–Teller (BET) method was used to determine the surface area of the nanofibers. Atomic force microscopy (AFM) was used to study the porosity and surface roughness of the nanofibers

Artificial intelligence for microscopy: what you should know

Artificial Intelligence based on Deep Learning (DL) is opening new horizons in biomedical research and promises to revolutionize the microscopy field. It is now transitioning from the hands of experts in computer sciences to biomedical researchers. Here, we introduce recent developments in DL applied to microscopy, in a manner accessible to non-experts. We give an overview of its concepts, capabilities and limitations, presenting applications in image segmentation, classification and restoration. We discuss how DL shows an outstanding potential to push the limits of microscopy, enhancing resolution, signal and information content in acquired data. Its pitfalls are discussed, along with the future directions expected in this field