A TMA De-Arraying Method for High Throughput Biomarker Discovery in Tissue Research

Background: Tissue MicroArrays (TMAs) represent a potential high-throughput platform for the analysis and discovery of tissue biomarkers. As TMA slides are produced manually and subject to processing and sectioning artefacts, the layout of TMA cores on the final slide and subsequent digital scan (TMA digital slide) is often disturbed making it difficult to associate cores with their original position in the planned TMA map. Additionally, the individual cores can be greatly altered and contain numerous irregularities such as missing cores, grid rotation and stretching. These factors demand the development of a robust method for de-arraying TMAs which identifies each TMA core, and assigns them to their appropriate coordinates on the constructed TMA slide.

Methodology: This study presents a robust TMA de-arraying method consisting of three functional phases: TMA core segmentation, gridding and mapping. The segmentation of TMA cores uses a set of morphological operations to identify each TMA core. Gridding then utilises a Delaunay Triangulation based method to find the row and column indices of each TMA core. Finally, mapping correlates each TMA core from a high resolution TMA whole slide image with its name within a TMAMap.

Conclusion: This study describes a genuine robust TMA de-arraying algorithm for the rapid identification of TMA cores from digital slides. The result of this de-arraying algorithm allows the easy partition of each TMA core for further processing. Based on a test group of 19 TMA slides (3129 cores), 99.84% of cores were segmented successfully, 99.81% of cores were gridded correctly and 99.96% of cores were mapped with their correct names via TMAMaps. The gridding of TMA cores were also extensively tested using a set of 113 pseudo slide (13,536 cores) with a variety of irregular grid layouts including missing cores, rotation and stretching. 100% of the cores were gridded correctly.

Playful structure: a novel image of early years pedagogy for primary school classrooms

Playful structure is a new pedagogic image representing a more balanced and integrated perspective on early years pedagogy, aiming to blend apparent dichotomies and contradictions and to sustain and evolve play-based practice beyond Year 1. Playful structure invites teachers and children to initiate and maintain a degree of playfulness in the child’s whole learning experience, even when the learning intentions demand a supportive structure. Thus, playfulness becomes characteristic of the interaction between adult and the child and not just characteristic of child-initiated versus adult-initiated activities, or of play-time versus task-time. The paper is based on intensive observations and interviews with teachers in Northern Ireland who participated in a play-based and informal curriculum. This paper explains how playful structure rests on complementary processes of infusion of structure into play-based activities and infusion of playfulness into more structured activities, illustrated by cameos. ‘Infusion’ suggests the subtle blending process that allows apparent dichotomies and contradictions to be resolved in practice.

Hybrid image/ray-shooting UHF radio propagation predictor for populated indoor environments

A novel model for indoor wireless communication, based on a dual image and ray-shooting approach, is presented. The model, capable of improved site-specific indoor propagation prediction, considers multiple human bodies moving within the environment. In a modern office at 2.45GHz, the combined effect of pedestrian traffic and a moving receiver causes rapid temporal fading of up to 30dB.

A Robust Co-Localisation Measurement Utilising Z-Stack Image Intensity Similarities for Biological Studies

Background: Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D) image stacks are biased by noise and cross-overs from non-consecutive planes.

Method: In this study, we have developed Co-localisation Intensity Coefficients (CICs) and Co-localisation Binary Coefficients (CBCs), which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises.

Results: The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.

Image processing chip for small object detection

A new, front-end image processing chip is presented for real-time small object detection. It has been implemented using a 0.6 µ, 3.3 V CMOS technology and operates on 10-bit input data at 54 megasamples per second. It occupies an area of 12.9 mm×13.6 mm (including pads), dissipates 1.5 W, has 92 I/O pins and is to be housed in a 160-pin ceramic quarter flat-pack. It performs both one- and two-dimensional FIR filtering and a multilayer perceptron (MLP) neural network function using a reconfigurable array of 21 multiplication-accumulation cells which corresponds to a window size of 7×3. The chip can cope with images of 2047 pixels per line and can be cascaded to cope with larger window sizes. The chip performs two billion fixed point multiplications and additions per second.

Applying an XC6200 to real-time image processing

This implementation of a two-dimensional discrete cosine transform demonstrates the development of a suitable architectural style for a specific technology-in this case, the Xilinx XC6200 FPGA series. The design exploits distributed arithmetic, parallelism, and pipelining to achieve a high-performance custom-computing implementation.

Image-Based Spatialization

An approach to spatialization is described in which the pixels of an image determine both spatial and other attributes of individual elements in a multi-channel musical texture. The application of this technique in the author’s composition Spaced Images with Noise and Lines is discussed in detail. The relationship of this technique to existing image-to-sound mappings is discussed. The particular advantage of modifying spatial properties with image filters is considered.

The Absent Image in Electronic Music

A survey of the after-effects of recording technology on media arts, particularly in the digital age. The article covers a wide variety of sound artists, including work by the author.