Improving statistics for hybrid segmentation of high-resolution multichannel images

High-resolution multichannel textures are difficult to characterize with simple statistics and the high level of detail makes the selection of a particular contour using classical gradient-based methods not effective. We have developed a hybrid method that combines fuzzy connectedness and Voronoi diagram classification for the segmentation of color and multichannel objects. The multi-step classification process relies on homogeneity measures derived from moment statistics and histogram information. These color features have been optimized to best combine individual channel information in the classification process. The segmentation initialization requires only a set of interior and exterior seed points, minimizing user intervention and the influence of the initialization on the overall quality of the results. The method was tested on volumes from the Visible Human and on brain multi-protocol MRI data sets. The hybrid segmentation produced robust, rapid and finely detailed contours with good visual accuracy. The addition of quantized statistics and color histogram distances as classification features improved the robustness of the method with regards to initialization when compared to our original implementation

International Federation of Clinical Neurophysiology (IFCN) – EEG research workgroup: Recommendations on frequency and topographic analysis of resting state EEG rhythms. Part 1: Applications in clinical research studies

In 1999, the International Federation of Clinical Neurophysiology (IFCN) published “IFCN Guidelines for topographic and frequency analysis of EEGs and EPs” (Nuwer et al., 1999). Here a Workgroup of IFCN experts presents unanimous recommendations on the following procedures relevant for the topographic and frequency analysis of resting state EEGs (rsEEGs) in clinical research defined as neurophysiological experimental studies carried out in neurological and psychiatric patients: (1) recording of rsEEGs (environmental conditions and instructions to participants; montage of the EEG electrodes; recording settings); (2) digital storage of rsEEG and control data; (3) computerized visualization of rsEEGs and control data (identification of artifacts and neuropathological rsEEG waveforms); (4) extraction of “synchronization” features based on frequency analysis (band-pass filtering and computation of rsEEG amplitude/power density spectrum); (5) extraction of “connectivity” features based on frequency analysis (linear and nonlinear measures); (6) extraction of “topographic” features (topographic mapping; cortical source mapping; estimation of scalp current density and dura surface potential; cortical connectivity mapping), and (7) statistical analysis and neurophysiological interpretation of those rsEEG features. As core outcomes, the IFCN Workgroup endorsed the use of the most promising “synchronization” and “connectivity” features for clinical research, carefully considering the limitations discussed in this paper. The Workgroup also encourages more experimental (i.e. simulation studies) and clinical research within international initiatives (i.e., shared software platforms and databases) facing the open controversies about electrode montages and linear vs. nonlinear and electrode vs. source levels of those analyses

Current Methods for Hyperpolarized [1-13C]pyruvate MRI Human Studies

MRI with hyperpolarized (HP) 13C agents, also known as HP 13C MRI, can measure processes such as localized metabolism that is altered in numerous cancers, liver, heart, kidney diseases, and more. It has been translated into human studies during the past 10 years, with recent rapid growth in studies largely based on increasing availability of hyperpolarized agent preparation methods suitable for use in humans. This paper aims to capture the current successful practices for HP MRI human studies with [1-13C]pyruvate - by far the most commonly used agent, which sits at a key metabolic junction in glycolysis. The paper is divided into four major topic areas: (1) HP 13C-pyruvate preparation, (2) MRI system setup and calibrations, (3) data acquisition and image reconstruction, and (4) data analysis and quantification. In each area, we identified the key components for a successful study, summarized both published studies and current practices, and discuss evidence gaps, strengths, and limitations. This paper is the output of the HP 13C MRI Consensus Group as well as the ISMRM Hyperpolarized Media MR and Hyperpolarized Methods & Equipment study groups. It further aims to provide a comprehensive reference for future consensus building as the field continues to advance human studies with this metabolic imaging modality

3D Architectural Analysis of Neurons, Astrocytes, Vasculature & Nuclei in the Motor and Somatosensory Murine Cortical Columns

Characterization of the complex cortical structure of the brain at a cellular level is a fundamental goal of neuroscience which can provide a better understanding of both normal function as well as disease state progression. Many challenges exist however when carrying out this form of analysis. Immunofluorescent staining is a key technique for revealing 3-dimensional structure, but subsequent fluorescence microscopy is limited by the quantity of simultaneous targets that can be labeled and intrinsic lateral and isotropic axial point-spread function (PSF) blurring during the imaging process in a spectral and depth-dependent manner. Even after successful staining, imaging and optical deconvolution, the sheer density of filamentous processes in the neuropil significantly complicates analysis due to the difficulty of separating individual cells in a highly interconnected network of tightly woven cellular arbors. In order to solve these problems, a variety of methodologies were developed and validated for improved analysis of cortical anatomy. An enhanced immunofluorescent staining and imaging protocol was utilized to precisely locate specific functional regions within brain slices at high magnification and collect four-channel, complete cortical columns. A powerful deconvolution routine was established which collected depth variant PSFs using an optical phantom for image restoration. Fractional volume analysis (FVA) was used to provide preliminary data of the proportions of each stained component in order to statistically characterize the variability within and between the functional regions in a depth-dependent and depth-independent manner. Finally, using machine learning techniques, a supervised learning model was developed that could automatically classify neuronal and astrocytic nuclei within the large cortical column datasets based on perinuclear fluorescence. These annotated nuclei were then used as seed points within their corresponding fluorescent channel for cell individualization in a highly interconnected network. For astrocytes, this technique provides the first method for characterization of complex morphology in an automated fashion over large areas without laborious dye filling or manual tracing

Classification software technique assessment

A catalog of software options is presented for the use of local user communities to obtain software for analyzing remotely sensed multispectral imagery. The resources required to utilize a particular software program are described. Descriptions of how a particular program analyzes data and the performance of that program for an application and data set provided by the user are shown. An effort is made to establish a statistical performance base for various software programs with regard to different data sets and analysis applications, to determine the status of the state-of-the-art

The fate of colors in the 20th - 21st centuries: preserving the organic colorants in plastic artifacts

Objectos modernos e contemporâneos feitos de plástico são amplamente encontrados no património cultural. Presentemente, a sua preservação levanta questões críticas aos conservadores e cientistas uma vez que estes objectos podem facilmente sofrer degradação num curto espaço de tempo. Um dos fenómenos que pode alterar significativamente a aparência de objectos em plástico é a alteração de cor (descoloração). De um modo geral, a descoloração é habitualmente associada à degradação dos polímeros, contudo, os pigmentos, que são parte integrante das formulações do plástico, também podem desvanecer devido à exposição à luz. A identificação de objetos de plástico com pigmentos sensíveis à luz é um exercício bastante exigente devido à sensibilidade dos mesmos a alterações na cor. A caracterização dos corantes nos plásticos é normalmente realizada através de amostragem, métodos de extração e testagem destrutiva. Como alternativa, esta tese apresenta uma abordagem inovadora e multi- analítica baseada em espectroscopias que foi desenvolvida para a identificação in situ dos pigmentos em plásticos históricos. Esta metodologia compreendeu a utilização de microscopia ótica (MO), microespectrometria por fluorescência de raios X dispersiva de energias (μ-EDXRF), espectroscopia UV-Vis-NIR de reflectância, fotoluminescência (PL) e micro-espectroscopia de Raman (μ-Raman) na análise de obras de arte, objetos industriais e de uso diário, datados de 1950-2000s e pertencentes a coleções Portuguesas. Deste estudo resultou a identificação dos pigmentos comumente presentes na paleta de cor dos coloristas da indústria dos plásticos portuguesa: óxido de ferro (PR 101, α-Fe2O3), molibdato de cromato de chumbo (PR 104, Pb(Cr,Mo,S)O4), vermelho de cádmio (PR 108, Cd(S,Se); PR 113, (Cd,Hg)S), amarelo de cádmio (PY 37, CdS; PY 35; (Cd,Zn)S), branco de titânio (PW 6, TiO2 ambos rutilo e anátase), oxicloreto de bismuto (PW 14, BiOCl) e lacas do pigmento orgânico β-naftol (PR 48, PR 49, PR 53). Adicionalmente, foi também identificado um pigmento fora do comum, o pigmento perlascente plumbonacrite Pb5(CO3)3O(OH)2. Para todos os casos de estudo, μ-Raman foi a ferramenta chave para a caracterização dos pigmentos nos objetos de plástico, aportando dados conclusivos para a identificação dos mesmos. A impressão digital vibracional dos pigmentos orgânicos e inorgânicos foi adquirida com sucesso recorrendo à focagem do laser na superfície das partículas. A aquisição de dados espectrais de pigmentos com concentrações muito baixas (0.1 % a 5%, aproximadamente) à escala micro foi possível através de microscopia confocal, que faz parte do sistema do equipamento de μ-Raman. Adicionalmente, foi também possível obter informação sobre o polímero base (principalmente termoplásticos) e cargas. Os métodos analíticos desenvolvidos neste estudo deverão, em trabalhos futuros, facilitar a obtenção de informação complementar sobre estes objetos de plástico e permitir uma melhor identificação e avaliação do seu estado de conservação. Esta tese foca particularmente objectos de plástico vermelhos visto que estes foram identificados como os mais severamente afetados por alterações de cor. O estado avançado de desvanecimento identificado no pigmento β-naftol PR 53 mostrou a sua fraca estabilidade à luz em formulações de plástico. Esta situação, junto com as alterações de cor descritas em literatura para o pigmento PR 48 em objetos de plástico, sugere uma sensibilidade dos pigmentos vermelhos da família dos β-naftol ao desvanecimento. O PR 53 e os pigmentos vermelhos da família dos β-naftóis são pigmentos históricos facilmente encontrados em objetos do património cultural. No entanto, o conhecimento acerca da sua estabilidade a longo prazo e resistência à foto-degradação é limitado, especialmente para os casos onde os mesmos se encontram em polímeros, sendo que este conhecimento é essencial para a sua preservação. Neste estudo, a quantificação da foto-estabilidade para uma série de pigmentos vermelhos da família dos β-naftol foi realizada pela primeira vez, através do cálculo do rendimento quântico de fotodegradação (ΦR). Os valores obtidos variaram entre 3x10-6 e 4x10-5, indicativo de uma estabilidade relativamente boa à luz por parte das moléculas. Tendo em consideração que a estabilidade dos pigmentos não se limita exclusivamente ao pigmento em si, mas também à sua interação com o meio envolvente, foram realizados ensaios de envelhecimento por exposição à luz (λ>300 nm) do pigmento em solução, em pó e incorporado em polímeros de modo a avaliar o papel do meio na estabilidade à luz dos pigmentos e as vias pelas quais estes se degradam. Verificou-se que o ligante tem um impacto significativo na estabilidade do pigmento uma vez que se foi detetada uma maior sensibilidade à luz dos pigmentos PR 48 e PR 53 quando incorporados nos plásticos, comparativamente ao ensaio do pigmento em pó. Este novo conhecimento irá contribuir para o desenvolvimento de novas estratégias na conservação dos plásticos com estes pigmentos vermelhos fotossensíveis através da previsão do desvanecimento. Espectrometrias de massa (MS) por cromatografia em fase líquida e gasosa foram utilizadas na caracterização dos principais subprodutos da degradação. Observou-se uma fotodegradação significativa e a formação de compostos ftálicos e ftalatos nos pigmentos em solução e em pó.Modern and contemporary objects made of plastics are widely found in cultural heritage. Today, their preser- vation poses critical issues to conservators and scientists, as they can suffer from extensive degradation in a short time period. Color change (discoloration) is one of the alteration phenomena that can significantly affect their appearance. Discoloration is commonly associated with the degradation of polymers. However, pigments within plastics can also fade due to exposure to light. The identification of objects that contain light-sensitive pigments is demanding because of the sensitivity of plastics to color change. Normally sampling, extraction methods and destructive testing are required for the characterization of colorants in plastics. In this work, an innovative multi-analytical spectroscopic approach for the in situ identification of pigments in historical plastics was developed. Optical microscopy (MO), micro-energy dispersive X-ray fluo- rescence (μ-EDXRF), UV-Vis-NIR reflectance, photoluminescence (PL) and Raman microscopy (μ-Raman), were used for the analysis of artworks, industrial and daily objects dated from 1950s-2000s from Portuguese collections. A common colorists’ palette within the Portuguese plastics industry was identified: iron oxide (PR 101, α-Fe2O3), lead chromate molybdate (PR 104, Pb(Cr,Mo,S)O4), cadmium red (PR 108, Cd(S,Se); PR 113, (Cd,Hg)S) and cadmium yellow (PY 37, CdS; PY 35; (Cd,Zn)S) pigments, titanium whites (PW 6, TiO2 both rutile and anatase), bismuth oxychloride (PW 14, BiOCl) and organic β-naphthol lakes (PR 48, PR 49, PR 53). An exceptional pigment found was the pearlescent plumbonacrite pigment Pb5(CO3)3O(OH)2. In all the case studies, μ-Raman was the key analytical tool for pigment characterization in the plastic objects, providing conclusive data for their identification. The vibrational fingerprint of both inorganic and organic pigments was successfully recorded by focusing the laser beam on particle surfaces. The confocal microscopy system used in μ-Raman enabled the collection of spectral data from low concentrations of pigments (ap- proximately 0.1%-5%) on the micro-scale. In addition to pigments, information on the base polymer (mainly thermoplastics) and fillers was obtained. The analytical methods developed will facilitate the acquisition of complementary data from plastics allowing material identification and condition assessment in the future. This thesis focused on red pigmented plastic artifacts, as they were found to be severely faded among the studied objects. The identification of β-naphthol pigment lake PR 53 as a faded pigment highlighted its poor fastness in plastics, that together with the color change of PR 48 in plastic objects, reported in literature, suggests the particular susceptibility of β-naphthol red lakes to fading. PR 53, and the other β-naphthol reds, are historical pigments widely found in cultural heritage. However, little is known about their photodegradation and stability, especially when they are found in polymer media, and this knowledge is essential for their long- term preservation. For the first time, photodegradation quantum yields (ΦR) were calculated for a series of red pigments based on β-naphthol in order to quantify their photo-stability. ΦR values ranging from 3x10-6 to 4x10-5 were obtained, indicating relatively light-stable molecules. Bearing in mind that pigment fastness is not only related to the pigment itself, but also to its interaction with the confined environment, light-aging experiments (λ>300 nm) were conducted in solution, on powders, and in polymers to assess the role of the medium on the lightfastness of the pigments and their degradation pathways. A significant impact of the binder on their stability was found. Indeed, a higher sensitivity to light of PR 48 and PR 53 pigments, when incorporated in plastics than in powder, was observed. This new knowledge will contribute to the prediction of plastic fading and inform effective preventive conservation strategies for objects containing light- sensitive β-naphthol red pigments. Liquid- and gas-chromatography mass spectrometry (MS) were used for the characterization of the main degradation products. Extensive photodegradation was observed with the formation of phthalic compounds and phthalates in both solution and powder phases

Catalog of Viking mission data

This catalog announces the present/expected availability of scientific data acquired by the Viking missions and contains descriptions of the Viking spacecraft, experiments, and data sets. An index is included listing the team leaders and team members for the experiments. Information on NSSDC facilities and ordering procedures, and a list of acronyms and abbreviations are included in the appendices