Analysis of population dispersion in histological sections

Stereology and other image analysis methods have enabled rapid and objective quantitative measurements to be made on histological sections. These mesurements may include total volumes, surfaces, lengths and numbers of cells and blood vessels or pathological lesions. Histological features, however, may not be randomly distributed across a section but exhibit 'dispersion', a departure from randomness either towards regularity or aggregation. Information of population dispersion may be valuable not only in understanding the two-or three-dimensional structure but also in elucidating the pathogenesis of lesions in pathological conditions. This article reviews some of the statistical methods available for studying dispersion. These range from simple tests of whether the distribution of a histological faeture departs significantly from random to more complex methods which can detect the intensity of aggregation and the sizes, distribution and spacing of the clusters.

An evaluation of task analysis techniques for industrial process control

The concept of a task is fundamental to the discipline of ergonomics. Approaches to the analysis of tasks began in the early 1900's. These approaches have evolved and developed to the present day, when there is a vast array of methods available. Some of these methods are specific to particular contexts or applications, others more general. However, whilst many of these analyses allow tasks to be examined in detail, they do not act as tools to aid the design process or the designer. The present thesis examines the use of task analysis in a process control context, and in particular the use of task analysis to specify operator information and display requirements in such systems. The first part of the thesis examines the theoretical aspect of task analysis and presents a review of the methods, issues and concepts relating to task analysis. A review of over 80 methods of task analysis was carried out to form a basis for the development of a task analysis method to specify operator information requirements in industrial process control contexts. Of the methods reviewed Hierarchical Task Analysis was selected to provide such a basis and developed to meet the criteria outlined for such a method of task analysis. The second section outlines the practical application and evolution of the developed task analysis method. Four case studies were used to examine the method in an empirical context. The case studies represent a range of plant contexts and types, both complex and more simple, batch and continuous and high risk and low risk processes. The theoretical and empirical issues are drawn together and a method developed to provide a task analysis technique to specify operator information requirements and to provide the first stages of a tool to aid the design of VDU displays for process control.

Contrast integration over area is extensive: a three-stage model of spatial summation

Classical studies of area summation measure contrast detection thresholds as a function of grating diameter. Unfortunately, (i) this approach is compromised by retinal inhomogeneity and (ii) it potentially confounds summation of signal with summation of internal noise. The Swiss cheese stimulus of T. S. Meese and R. J. Summers (2007) and the closely related Battenberg stimulus of T. S. Meese (2010) were designed to avoid these problems by keeping target diameter constant and modulating interdigitated checks of first-order carrier contrast within the stimulus region. This approach has revealed a contrast integration process with greater potency than the classical model of spatial probability summation. Here, we used Swiss cheese stimuli to investigate the spatial limits of contrast integration over a range of carrier frequencies (1–16 c/deg) and raised plaid modulator frequencies (0.25–32 cycles/check). Subthreshold summation for interdigitated carrier pairs remained strong (~4 to 6 dB) up to 4 to 8 cycles/check. Our computational analysis of these results implied linear signal combination (following square-law transduction) over either (i) 12 carrier cycles or more or (ii) 1.27 deg or more. Our model has three stages of summation: short-range summation within linear receptive fields, medium-range integration to compute contrast energy for multiple patches of the image, and long-range pooling of the contrast integrators by probability summation. Our analysis legitimizes the inclusion of widespread integration of signal (and noise) within hierarchical image processing models. It also confirms the individual differences in the spatial extent of integration that emerge from our approach.

A quantitative analysis of optic nerve axons in elderly control subjects and patients with Alzheimer's disease

Objective: To study the density and cross-sectional area of axons in the optic nerve in elderly control subjects and in cases of Alzheimer's disease (AD) using an image analysis system. Methods: Sections of optic nerves from control and AD patients were stained with toluidine blue to reveal axon profiles. Results: The density of axons was reduced in both the center and peripheral portions of the optic nerve in AD compared with control patients. Analysis of axons with different cross-sectional areas suggested a specific loss of the smaller sized axons in AD, i.e., those with areas less that 1.99 μm2. An analysis of axons >11 μm2 in cross-sectional area suggested no specific loss of the larger axons in this group of patients. Conclusions: The data suggest that image analysis provides an accurate and reproducible method of quantifying axons in the optic nerve. In addition, the data suggest that axons are lost throughout the optic nerve with a specific loss of the smaller-sized axons. Loss of the smaller axons may explain the deficits in color vision observed in a significant proportion of patients with AD.

Task-based annotation and retrieval for image information management

Continuing advances in digital image capture and storage are resulting in a proliferation of imagery and associated problems of information overload in image domains. In this work we present a framework that supports image management using an interactive approach that captures and reuses task-based contextual information. Our framework models the relationship between images and domain tasks they support by monitoring the interactive manipulation and annotation of task-relevant imagery. During image analysis, interactions are captured and a task context is dynamically constructed so that human expertise, proficiency and knowledge can be leveraged to support other users in carrying out similar domain tasks using case-based reasoning techniques. In this article we present our framework for capturing task context and describe how we have implemented the framework as two image retrieval applications in the geo-spatial and medical domains. We present an evaluation that tests the efficiency of our algorithms for retrieving image context information and the effectiveness of the framework for carrying out goal-directed image tasks. © 2010 Springer Science+Business Media, LLC.

Quantitative analysis of multi-spectral fundus images

We have developed a new technique for extracting histological parameters from multi-spectral images of the ocular fundus. The new method uses a Monte Carlo simulation of the reflectance of the fundus to model how the spectral reflectance of the tissue varies with differing tissue histology. The model is parameterised by the concentrations of the five main absorbers found in the fundus: retinal haemoglobins, choroidal haemoglobins, choroidal melanin, RPE melanin and macular pigment. These parameters are shown to give rise to distinct variations in the tissue colouration. We use the results of the Monte Carlo simulations to construct an inverse model which maps tissue colouration onto the model parameters. This allows the concentration and distribution of the five main absorbers to be determined from suitable multi-spectral images. We propose the use of "image quotients" to allow this information to be extracted from uncalibrated image data. The filters used to acquire the images are selected to ensure a one-to-one mapping between model parameters and image quotients. To recover five model parameters uniquely, images must be acquired in six distinct spectral bands. Theoretical investigations suggest that retinal haemoglobins and macular pigment can be recovered with RMS errors of less than 10%. We present parametric maps showing the variation of these parameters across the posterior pole of the fundus. The results are in agreement with known tissue histology for normal healthy subjects. We also present an early result which suggests that, with further development, the technique could be used to successfully detect retinal haemorrhages.

Comparison between graticule and image capture assessment of lower tear film meniscus height

Purpose: To compare graticule and image capture assessment of the lower tear film meniscus height (TMH). Methods: Lower tear film meniscus height measures were taken in the right eyes of 55 healthy subjects at two study visits separated by 6 months. Two images of the TMH were captured in each subject with a digital camera attached to a slit-lamp biomicroscope and stored in a computer for future analysis. Using the best of two images, the TMH was quantified by manually drawing a line across the tear meniscus profile, following which the TMH was measured in pixels and converted into millimetres, where one pixel corresponded to 0.0018 mm. Additionally, graticule measures were carried out by direct observation using a calibrated graticule inserted into the same slit-lamp eyepiece. The graticule was calibrated so that actual readings, in 0.03 mm increments, could be made with a 40× ocular. Results: Smaller values of TMH were found in this study compared to previous studies. TMH, as measured with the image capture technique (0.13 ± 0.04 mm), was significantly greater (by approximately 0.01 ± 0.05 mm, p = 0.03) than that measured with the graticule technique (0.12 ± 0.05 mm). No bias was found across the range sampled. Repeatability of the TMH measurements taken at two study visits showed that graticule measures were significantly different (0.02 ± 0.05 mm, p = 0.01) and highly correlated (r = 0.52, p < 0.0001), whereas image capture measures were similar (0.01 ± 0.03 mm, p = 0.16), and also highly correlated (r = 0.56, p < 0.0001). Conclusions: Although graticule and image analysis techniques showed similar mean values for TMH, the image capture technique was more repeatable than the graticule technique and this can be attributed to the higher measurement resolution of the image capture (i.e. 0.0018 mm) compared to the graticule technique (i.e. 0.03 mm). © 2006 British Contact Lens Association.

The effect of digital image resolution and compression on anterior eye imaging

Aim: To determine the theoretical and clinical minimum image pixel resolution and maximum compression appropriate for anterior eye image storage. Methods: Clinical images of the bulbar conjunctiva, palpebral conjunctiva, and corneal staining were taken at the maximum resolution of Nikon:CoolPix990 (2048 × 1360 pixels), DVC:1312C (1280 × 811), and JAI:CV-S3200 (767 × 569) single chip cameras and the JVC:KYF58 (767 × 569) three chip camera. The images were stored in TIFF format and further copies created with reduced resolution or compressed. The images were then ranked for clarity on a 15 inch monitor (resolution 1280 × 1024) by 20 optometrists and analysed by objective image analysis grading. Theoretical calculation of the resolution necessary to detect the smallest objects of clinical interest was also conducted. Results: Theoretical calculation suggested that the minimum resolution should be ≥579 horizontal pixels at 25 × magnification. Image quality was perceived subjectively as being reduced when the pixel resolution was lower than 767 × 569 (p<0.005) or the image was compressed as a BMP or <50% quality JPEG (p<0.005). Objective image analysis techniques were less susceptible to changes in image quality, particularly when using colour extraction techniques. Conclusion: It is appropriate to store anterior eye images at between 1280 × 811 and 767 × 569 pixel resolution and at up to 1:70 JPEG compression.

Multispectral fundus analysis

Purpose - To generate a reflectance model of the fundus that allows an accurate non-invasive quantification of blood and pigments. Methods - A Monte Carlo simulation was used to produce a mathematical model of light interaction with the fundus at different wavelengths. The model predictions were compared with fundus images from normal volunteers in several spectral bands (peaks at 507, 525, 552, 585, 596 and 611nm). Th e model was then used to calculate the concentration and distribution of the known absorbing components of the fundus. Results - The shape of the statistical distribution of the image data generally corresponded to that of the model data; the model however appears to overestimate the reflectance of the fundus in the longer wavelength region.As the absorption by xanthophyll has no significant eff ect on light transport above 534nm, its distribution in the fundus was quantified: the wavelengths where both shape and distribution of image and model data matched (<553nm) were used to train a neural network which was then applied to every point in the image data. The xanthophyll distribution thus found was in agreement with published literature data in normal subjects. Conclusion - We have developed a method for optimising multi-spectral imaging of the fundus and a computer image analysis capable of estimating information about the structure and properties of the fundus. Th e technique successfully calculates the distribution of xanthophyll in the fundus of healthy volunteers. Further improvement of the model is required to allow the deduction of other parameters from images; investigations in known pathology models are also necessary to establish if this method is of clinical use in detecting early chroido-retinopathies, hence providing a useful screening and diagnostic tool.

Analysis of the Distributions of Color Characteristics in Art Painting Images

In this paper we study some of the characteristics of the art painting image color semantics. We analyze the color features of differ- ent artists and art movements. The analysis includes exploration of hue, saturation and luminance. We also use quartile’s analysis to obtain the dis- tribution of the dispersion of defined groups of paintings and measure the degree of purity for these groups. A special software system “Art Paint- ing Image Color Semantics” (APICSS) for image analysis and retrieval was created. The obtained result can be used for automatic classification of art paintings in image retrieval systems, where the indexing is based on color characteristics.

Objective analysis of contact lens fit

Purpose: To assess the validity and repeatability of objective compared to subjective contact lens fit analysis. Methods: Thirty-five subjects (aged 22.0. ±. 3.0 years) wore two different soft contact lens designs. Four lens fit variables: centration, horizontal lag, post-blink movement in up-gaze and push-up recovery speed were assessed subjectively (four observers) and objectively from slit-lamp biomicroscopy captured images and video. The analysis was repeated a week later. Results: The average of the four experienced observers was compared to objective measures, but centration, movement on blink, lag and push-up recovery speed all varied significantly between them (p <. 0.001). Horizontal lens centration was on average close to central as assessed both objectively and subjectively (p > 0.05). The 95% confidence interval of subjective repeatability was better than objective assessment (±0.128. mm versus ±0.168. mm, p = 0.417), but utilised only 78% of the objective range. Vertical centration assessed objectively showed a slight inferior decentration (0.371. ±. 0.381. mm) with good inter- and intrasession repeatability (p > 0.05). Movement-on-blink was lower estimated subjectively than measured objectively (0.269. ±. 0.179. mm versus 0.352. ±. 0.355. mm; p = 0.035), but had better repeatability (±0.124. mm versus ±0.314. mm 95% confidence interval) unless correcting for the smaller range (47%). Horizontal lag was lower estimated subjectively (0.562. ±. 0.259. mm) than measured objectively (0.708. ±. 0.374. mm, p <. 0.001), had poorer repeatability (±0.132. mm versus ±0.089. mm 95% confidence interval) and had a smaller range (63%). Subjective categorisation of push-up speed of recovery showed reasonable differentiation relative to objective measurement (p <. 0.001). Conclusions: The objective image analysis allows an accurate, reliable and repeatable assessment of soft contact lens fit characteristics, being a useful tool for research and optimisation of lens fit in clinical practice.

Habitat Map for Lizard Island reef, Australia derived from a photo-transect survey field data collected in December 2011 and September/October 2012

An object based image analysis approach (OBIA) was used to create a habitat map of the Lizard Reef. Briefly, georeferenced dive and snorkel photo-transect surveys were conducted at different locations surrounding Lizard Island, Australia. For the surveys, a snorkeler or diver swam over the bottom at a depth of 1-2m in the lagoon, One Tree Beach and Research Station areas, and 7m depth in Watson's Bay, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type using a benthic cover type classification scheme containing nine first-level categories - seagrass high (>=70%), seagrass moderate (40-70%), seagrass low (<= 30%), coral, reef matrix, algae, rubble, rock and sand. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. The OBIA class assignment followed a hierarchical assignment based on membership rules with levels for "reef", "geomorphic zone" and "benthic community" (above).

Habitat map of Danajon Bank, Philippines, derived from a high-spatial-resolution multi-spectral satellite image and georeferenced point intercept transect and spot-check survey field data, using an object-based image classification method

A mosaic of two WorldView-2 high resolution multispectral images (Acquisition dates: October 2010 and April 2012), in conjunction with field survey data, was used to create a habitat map of the Danajon Bank, Philippines (10°15'0'' N, 124°08'0'' E) using an object-based approach. To create the habitat map, we conducted benthic cover (seafloor) field surveys using two methods. Firstly, we undertook georeferenced point intercept transects (English et al., 1997). For ten sites we recorded habitat cover types at 1 m intervals on 10 m long transects (n= 2,070 points). Second, we conducted geo-referenced spot check surveys, by placing a viewing bucket in the water to estimate the percent cover benthic cover types (n = 2,357 points). Survey locations were chosen to cover a diverse and representative subset of habitats found in the Danajon Bank. The combination of methods was a compromise between the higher accuracy of point intercept transects and the larger sample area achievable through spot check surveys (Roelfsema and Phinn, 2008, doi:10.1117/12.804806). Object-based image analysis, using the field data as calibration data, was used to classify the image mosaic at each of the reef, geomorphic and benthic community levels. The benthic community level segregated the image into a total of 17 pure and mixed benthic classes.

An analysis of facial description in static images and video streams

[ES]This paper describes an analysis performed for facial description in static images and video streams. The still image context is first analyzed in order to decide the optimal classifier configuration for each problem: gender recognition, race classification, and glasses and moustache presence. These results are later applied to significant samples which are automatically extracted in real-time from video streams achieving promising results in the facial description of 70 individuals by means of gender, race and the presence of glasses and moustache.

Hierarchical clustering with multiple-height branch-cut applied to short time-series gene expression data.

Rigid adherence to pre-specified thresholds and static graphical representations can lead to incorrect decisions on merging of clusters. As an alternative to existing automated or semi-automated methods, we developed a visual analytics approach for performing hierarchical clustering analysis of short time-series gene expression data. Dynamic sliders control parameters such as the similarity threshold at which clusters are merged and the level of relative intra-cluster distinctiveness, which can be used to identify "weak-edges" within clusters. An expert user can drill down to further explore the dendrogram and detect nested clusters and outliers. This is done by using the sliders and by pointing and clicking on the representation to cut the branches of the tree in multiple-heights. A prototype of this tool has been developed in collaboration with a small group of biologists for analysing their own datasets. Initial feedback on the tool has been positive.