An R Library for Compositional Data Analysis in Archaeometry

Compositional data naturally arises from the scientific analysis of the chemicalcomposition of archaeological material such as ceramic and glass artefacts. Data of thistype can be explored using a variety of techniques, from standard multivariate methodssuch as principal components analysis and cluster analysis, to methods based upon theuse of log-ratios. The general aim is to identify groups of chemically similar artefactsthat could potentially be used to answer questions of provenance.This paper will demonstrate work in progress on the development of a documentedlibrary of methods, implemented using the statistical package R, for the analysis ofcompositional data. R is an open source package that makes available very powerfulstatistical facilities at no cost. We aim to show how, with the aid of statistical softwaresuch as R, traditional exploratory multivariate analysis can easily be used alongside, orin combination with, specialist techniques of compositional data analysis.The library has been developed from a core of basic R functionality, together withpurpose-written routines arising from our own research (for example that reported atCoDaWork'03). In addition, we have included other appropriate publicly availabletechniques and libraries that have been implemented in R by other authors. Availablefunctions range from standard multivariate techniques through to various approaches tolog-ratio analysis and zero replacement. We also discuss and demonstrate a smallselection of relatively new techniques that have hitherto been little-used inarchaeometric applications involving compositional data. The application of the libraryto the analysis of data arising in archaeometry will be demonstrated; results fromdifferent analyses will be compared; and the utility of the various methods discussed

Particle shape and orientation in laser diffraction and static image analysis size distribution analysis of micrometer sized rectangular particles

Laser diffraction (LD) and static image analysis (SIA) of rectangular particles [United States Pharmacopeia, USP30-NF25, General Chapter <776>, Optical Miroscopy.] have been systematically studied. To rule out sample dispersion and particle orientation as the root cause of differences in size distribution profiles, we immobilize powder samples on a glass plate by means of a dry disperser. For a defined region of the glass plate, we measure the diffraction pattern as induced by the dispersed particles, and the 2D dimensions of the individual particles using LD and optical microscopy, respectively. We demonstrate a correlation between LD and SIA, with the scattering intensity of the individual particles as the dominant factor. In theory, the scattering intensity is related to the square of the projected area of both spherical and rectangular particles. In traditional LD the size distribution profile is dominated by the maximum projected area of the particles (A). The diffraction diameters of a rectangular particle with length L and breadth B as measured by the LD instrument approximately correspond to spheres of diameter ØL and ØB respectively. Differences in the scattering intensity between spherical and rectangular particles suggest that the contribution made to the overall LD volume probability distribution by each rectangular particle is proportional to A2/L and A2/B. Accordingly, for rectangular particles the scattering intensity weighted diffraction diameter (SIWDD) explains an overestimation of their shortest dimension and an underestimation of their longest dimension. This study analyzes various samples of particles whose length ranges from approximately 10 to 1000 μm. The correlation we demonstrate between LD and SIA can be used to improve validation of LD methods based on SIA data for a variety of pharmaceutical powders all with a different rectangular particle size and shape.

Analysis of resuspension and sedimentation processes of unaltered fish faeces using image analysis

Postprint (published version)

Improving the oscillating grid method to characterize aquaculture biosolids using a laser beam and image analysis

Quickremovalofbiosolidsinaquaculturefacilities,andspeciallyinrecirculatingaquaculturesystems(RAS),isoneofthemostimportantstepinwastemanagement.Sedimentationdynamicsofbiosolidsinanaquaculturetankwilldeterminetheiraccumulationatthebottomofthetank.

Segmentació d'imatge de ressonància magnètica de pit utilitzant atlas probabilístic

La localització d'òrgans és un tòpic important en l'àmbit de la imatge mèdica per l'ajuda del tractament i diagnosi del càncer. Un exemple es pot trobar en la cal•libració de models farmacoquinètics. Aquesta pot ésser realitzada utilitzant un teixit de referència, on, per exemple en imatges de ressonància magnètica de pit, una correcta segmentació del múscul pectoral és necessària per a la detecció de signes de malignitat. Els mètodes de segmentació basat en atlas han estat altament avaluats en imatge de ressonància magnètica de cervell, obtenint resultats satisfactoris. En aquest projecte, en col•laboració amb el el Diagnostic Image Analysis Group de la Radboud University Nijmegen Medical Centre i la supervisió del Dr. N.Karssemeijer, es presenta la primera aproximació d'un mètode de segmentació basat en atlas per segmentar els diferents teixits visibles en imatges de ressonància magnètica (T1) del pit femení. L'atlas consisteix en 5 estructures (teixit greixòs, teixit dens, cor, pulmons i múscul pectoral) i ha estat utilitzat en un algorisme de segmentació Bayesià per tal de delinear les esmentades estructures. A més a més, s'ha dut a terme una comparació entre un mètode de registre global i un de local, utilitzats tant en la construcció de l'atlas com en la fase de segmentació, essent el primer el que ha presentat millors resultats en termes d'eficiència i precisió. Per a l'avaluació, s'ha dut a terme una comparació visual i numèrica entre les segmentacions obtingudes i les realitzades manualment pels experts col•laboradors. Pel que fa a la numèrica, s'ha emprat el coeficient de similitud de Dice ( mesura que dóna valors entre 0 i 1, on 0 significa no similitud i 1 similitud màxima) i s'ha obtingut una mitjana general de 0.8. Aquest resultat confirma la validesa del mètode presentat per a la segmentació d'imatges de ressonància magnètica del pit.

Compression-based Image Registration

Image registration is an important component of image analysis used to align two or more images. In this paper, we present a new framework for image registration based on compression. The basic idea underlying our approach is the conjecture that two images are correctly registered when we can maximally compress one image given the information in the other. The contribution of this paper is twofold. First, we show that the image registration process can be dealt with from the perspective of a compression problem. Second, we demonstrate that the similarity metric, introduced by Li et al., performs well in image registration. Two different versions of the similarity metric have been used: the Kolmogorov version, computed using standard real-world compressors, and the Shannon version, calculated from an estimation of the entropy rate of the images

Transketolase-like 1 expression is modulated during Colorectal cancer progression and metastasis formation

Background Transketolase-like 1 (TKTL1) induces glucose degradation through anaerobic pathways, even in presence of oxygen, favoring the malignant aerobic glycolytic phenotype characteristic of tumor cells. As TKTL1 appears to be a valid biomarker for cancer prognosis, the aim of the current study was to correlate its expression with tumor stage, probability of tumor recurrence and survival, in a series of colorectal cancer patients. Methodolody/Principal Findings Tumor tissues from 63 patients diagnosed with colorectal cancer at different stages of progression were analyzed for TKTL1 by immunohistochemistry. Staining was quantified by computational image analysis, and correlations between enzyme expression, local growth, lymph-node involvement and metastasis were assessed. The highest values for TKTL1 expression were detected in the group of stage III tumors, which showed significant differences from the other groups (Kruskal-Wallis test, P = 0.000008). Deeper analyses of T, N and M classifications revealed a weak correlation between local tumor growth and enzyme expression (Mann-Whitney test, P = 0.029), a significant association of the enzyme expression with lymph-node involvement (Mann-Whitney test, P = 0.0014) and a significant decrease in TKTL1 expression associated with metastasis (Mann-Whitney test, P = 0.0004). Conclusions/Significance To our knowledge, few studies have explored the association between variations in TKTL1 expression in the primary tumor and metastasis formation. Here we report downregulation of enzyme expression when metastasis appears, and a correlation between enzyme expression and regional lymph-node involvement in colon cancer. This finding may improve our understanding of metastasis and lead to new and more efficient therapies against cancer.

Nuclear DNA content variation in life history phases of the Bonnemaisoniaceae (Rhodophyta)

Nuclear DNA content in gametophytes and sporophytes or the prostrate phases of the following species of Bonnemaisoniaceae (Asparagopsis armata, Asparagopsis taxiformis, Bonnemaisonia asparagoides, Bonnemaisonia clavata and Bonnemaisonia hamifera) were estimated by image analysis and static microspectrophotometry using the DNA-localizing fluorochrome DAPI (4′, 6-diamidino-2-phenylindole, dilactate) and the chicken erythrocytes standard. These estimates expand on the Kew database of DNA nuclear content. DNA content values for 1C nuclei in the gametophytes (spermatia and vegetative cells) range from 0.5 pg to 0.8 pg, and for 2C nuclei in the sporophytes or the prostrate phases range from 1.15-1.7 pg. Although only the 2C and 4C values were observed in the sporophyte or the prostrate phase, in the vegetative cells of the gametophyte the values oscillated from 1C to 4C, showing the possible start of endopolyploidy. The results confirm the alternation of nuclear phases in these Bonnemaisoniaceae species, in those that have tetrasporogenesis, as well as those that have somatic meiosis. The availability of a consensus phylogenetic tree for Bonnemaisoniaceae has opened the way to determine evolutionary trends in DNA contents. Both the estimated genome sizes and the published chromosome numbers for Bonnemaisoniaceae suggest a narrow range of values consistent with the conservation of an ancestral genome.

Programa d'anàlisi d'imatges de provetes metal·logràfiques

L’objectiu del present TFM és explorar les possibilitats del programa matemàtic MATLAB i la seva eina Entorn de Disseny d’Interfícies Gràfiques d’Usuari (GUIDE), desenvolupant un programa d’anàlisi d’imatges de provetes metal·logràfiques que es pugui utilitzar per a realitzar pràctiques de laboratori de l’assignatura Tecnologia de Materials de la titulació de Grau en Enginyeria Mecatrònica que s’imparteix a la Universitat de Vic. Les àrees d’interès del treball són la Instrumentació Virtual, la programació MATLAB i les tècniques d’anàlisi d’imatges metal·logràfiques. En la memòria es posa un èmfasi especial en el disseny de la interfície i dels procediments per a efectuar les mesures. El resultat final és un programa que satisfà tots els requeriments que s’havien imposat en la proposta inicial. La interfície del programa és clara i neta, destinant molt espai a la imatge que s’analitza. L’estructura i disposició dels menús i dels comandaments ajuda a que la utilització del programa sigui fàcil i intuïtiva. El programa s’ha estructurat de manera que sigui fàcilment ampliable amb altres rutines de mesura, o amb l’automatització de les rutines existents. Al tractar-se d’un programa que funciona com un instrument de mesura, es dedica un capítol sencer de la memòria a mostrar el procediment de càlcul dels errors que s’ocasionen durant la seva utilització, amb la finalitat de conèixer el seu ordre de magnitud, i de saber-los calcular de nou en cas que variïn les condicions d’utilització. Pel que fa referència a la programació, malgrat que MATLAB no sigui un entorn de programació clàssic, sí que incorpora eines que permeten fer aplicacions no massa complexes, i orientades bàsicament a gràfics o a imatges. L’eina GUIDE simplifica la realització de la interfície d’usuari, malgrat que presenta problemes per tractar dissenys una mica complexos. Per altra banda, el codi generat per GUIDE no és accessible, cosa que no permet modificar manualment la interfície en aquells casos en els que GUIDE té problemes. Malgrat aquests petits problemes, la potència de càlcul de MATLAB compensa sobradament aquestes deficiències.

Dynamics of flow: a nonlinear perspective

The aims of this study are to consider the experience of flow from a nonlinear dynamics perspective. The processes and temporal nature of intrinsic motivation and flow, would suggest that flow experiences fluctuate over time in a dynamical fashion. Thus it can be argued that the potential for chaos is strong. The sample was composed of 20 employees (both full and part time) recruited from a number of different organizations and work backgrounds. The Experience Sampling Method (ESM) was used for data collection. Once obtained the temporal series, they were subjected to various analyses proper to the com- plexity theory (Visual Recurrence Analysis and Surrogate Data Analysis). Results showed that in 80% of the cases, flow presented a chaotic dynamic, in that, flow experiences delineated a complex dynamic whose patterns of change were not easy to predict. Implications of the study, its limitations and future research are discussed.

Studies on the characterization of dental whitening process by using both hyperspectral imaging and colorimeter techniques

A beautiful smile is directly related with white teeth. Nowadays oral care has increased and developed processes for beautiful smiles. Dental bleaching is frequently used in odontology, not just for health care also for aesthetic treatment. With the possibility of teeth bleaching, now the importance is in, how white the tooth is? Because color is relate to an individual perception. In order to assets teeth correct color identification has been developed many color guides, models, spaces and analytical methods. Spite all of these useful tools the color interpretation depends on environmental factors, position of the sample in the data acquisition and most importantly the instrument sensitivity. The commons methods have proved to be useful. They are easy to handle, some are portable but they do not have a high sensitivity. The present work is based on the integration of a new analytical technique for color acquisition. High spectral Image (HSI) is able to performed image analysis with high quality and efficiency. HSI is used in many fields and we used it for color image analysis within the bleaching process. The main comparison was done with the HSI and the colorimeter through the processes of two different bleaching protocols. The results showed that HSI has higher sensitivity than the colorimeter. During the analysis the dental surface with the HSI we were able to notice surface changes. These changes were analyzed by roughness studies.

Blood pressure levels and haematoma growth in patients with Intracerebral Haemorrhage (ICH) A retrospective observational study

Intracerebral haemorrhage (ICH) is a spontaneous extravasation of blood into brain parenchyma. Although ICH represents approximately only 15% of all strokes, it is one of the major causes of stroke-related death and disability. One of the causes of poor outcome is the haematoma growth. The association between elevated blood pressure (BP) and haematoma enlargement in acute ICH has not been clarified. Our objective is to try to identify this relationship that may suggest an immediate target for intervention to possibly improve outcomes in patients with spontaneous ICH and might settle the controversy surrounding the optimal management of blood pressure.We propose a retrospective revision using a sample present in our database of approximately 250 patients with primary ICH and less than 12h from symptoms onset. Systolic blood pressure levels (SBP) are assessed at baseline, at 6h, at 12h, at 24h and at 72h, being these last four the average levels of the different recordings during those time intervals. Haematoma growth will be defined as an increase in the volume of intraparenchymal haemorrhage of >33% as measured by image analysis on the 24-hour CT or 72-hour CT compared with the baseline CT scan. A qualified neuroradiologist not informed of the aim of the study, will review the CT images. The secondary objective will be to correlate the BP levels in the acute phase of ICH with clinical outcome. We will evaluate early neurologic deterioration at 72h by using the National Institutes of Health Stroke Scale (NIHSS); outcome at 90 days by using the modified Rankin scale and mortality at 72h and 90 days. The statistical analysis will be adjusted by possibly confounding variables

Threshold Selection Criteria for Quantification of Lumbosacral Cerebrospinal Fluid and Root Volumes from MRI

BACKGROUND AND PURPOSE: The high variability of CSF volumes partly explains the inconsistency of anesthetic effects, but may also be due to image analysis itself. In this study, criteria for threshold selection are anatomically defined. METHODS: T2 MR images (n = 7 cases) were analyzed using 3-dimentional software. Maximal-minimal thresholds were selected in standardized blocks of 50 slices of the dural sac ending caudally at the L5-S1 intervertebral space (caudal blocks) and middle L3 (rostral blocks). Maximal CSF thresholds: threshold value was increased until at least one voxel in a CSF area appeared unlabeled and decreased until that voxel was labeled again: this final threshold was selected. Minimal root thresholds: thresholds values that selected cauda equina root area but not adjacent gray voxels in the CSF-root interface were chosen. RESULTS: Significant differences were found between caudal and rostral thresholds. No significant differences were found between expert and nonexpert observers. Average max/min thresholds were around 1.30 but max/min CSF volumes were around 1.15. Great interindividual CSF volume variability was detected (max/min volumes 1.6-2.7). CONCLUSIONS: The estimation of a close range of CSF volumes which probably contains the real CSF volume value can be standardized and calculated prior to certain intrathecal procedures

Programa d'anàlisi d'imatges de provetes metal·logràfiques

L’objectiu del present TFM és explorar les possibilitats del programa matemàtic MATLAB i la seva eina Entorn de Disseny d’Interfícies Gràfiques d’Usuari (GUIDE), desenvolupant un programa d’anàlisi d’imatges de provetes metal·logràfiques que es pugui utilitzar per a realitzar pràctiques de laboratori de l’assignatura Tecnologia de Materials de la titulació de Grau en Enginyeria Mecatrònica que s’imparteix a la Universitat de Vic. Les àrees d’interès del treball són la Instrumentació Virtual, la programació MATLAB i les tècniques d’anàlisi d’imatges metal·logràfiques. En la memòria es posa un èmfasi especial en el disseny de la interfície i dels procediments per a efectuar les mesures. El resultat final és un programa que satisfà tots els requeriments que s’havien imposat en la proposta inicial. La interfície del programa és clara i neta, destinant molt espai a la imatge que s’analitza. L’estructura i disposició dels menús i dels comandaments ajuda a que la utilització del programa sigui fàcil i intuïtiva. El programa s’ha estructurat de manera que sigui fàcilment ampliable amb altres rutines de mesura, o amb l’automatització de les rutines existents. Al tractar-se d’un programa que funciona com un instrument de mesura, es dedica un capítol sencer de la memòria a mostrar el procediment de càlcul dels errors que s’ocasionen durant la seva utilització, amb la finalitat de conèixer el seu ordre de magnitud, i de saber-los calcular de nou en cas que variïn les condicions d’utilització. Pel que fa referència a la programació, malgrat que MATLAB no sigui un entorn de programació clàssic, sí que incorpora eines que permeten fer aplicacions no massa complexes, i orientades bàsicament a gràfics o a imatges. L’eina GUIDE simplifica la realització de la interfície d’usuari, malgrat que presenta problemes per tractar dissenys una mica complexos. Per altra banda, el codi generat per GUIDE no és accessible, cosa que no permet modificar manualment la interfície en aquells casos en els que GUIDE té problemes. Malgrat aquests petits problemes, la potència de càlcul de MATLAB compensa sobradament aquestes deficiències.