FISHji: new ImageJ macros for the quantification of fluorescence in epifluorescence images

Fluorescence in situ hybridization (FISH) is based on the use of fluorescent staining dyes, however, the signal intensity of the images obtained by microscopy is seldom quantified with accuracy by the researcher. The development of innovative digital image processing programs and tools has been trying to overcome this problem, however, the determination of fluorescent intensity in microscopy images still has issues due to the lack of precision in the results and the complexity of existing software. This work presents FISHji, a set of new ImageJ methods for automated quantification of fluorescence in images obtained by epifluorescence microscopy. To validate the methods, results obtained by FISHji were compared with results obtained by flow cytometry. The mean correlation between FISHji and flow cytometry was high and significant, showing that the imaging methods are able to accurately assess the signal intensity of fluorescence images. FISHji are available for non-commercial use at http://paginas.fe.up.pt/nazevedo/.

Automating the testing process of image processing algorithms

As digital imaging processing techniques become increasingly used in a broad range of consumer applications, the critical need to evaluate algorithm performance has become recognised by developers as an area of vital importance. With digital image processing algorithms now playing a greater role in security and protection applications, it is of crucial importance that we are able to empirically study their performance. Apart from the field of biometrics little emphasis has been put on algorithm performance evaluation until now and where evaluation has taken place, it has been carried out in a somewhat cumbersome and unsystematic fashion, without any standardised approach. This paper presents a comprehensive testing methodology and framework aimed towards automating the evaluation of image processing algorithms. Ultimately, the test framework aims to shorten the algorithm development life cycle by helping to identify algorithm performance problems quickly and more efficiently.

Hardcopy quality parameters to ensure structures detection at digital mammography

Objective To develop procedures to ensure consistency of printing quality of digital images, by means of hardcopy quantitative analysis based on a standard image. Materials and Methods Characteristics of mammography DI-ML and general purpose DI-HL films were studied through the QC-Test utilizing different processing techniques in a FujiFilm®-DryPix4000 printer. A software was developed for sensitometric evaluation, generating a digital image including a gray scale and a bar pattern to evaluate contrast and spatial resolution. Results Mammography films showed maximum optical density of 4.11 and general purpose films, 3.22. The digital image was developed with a 33-step wedge scale and a high-contrast bar pattern (1 to 30 lp/cm) for spatial resolution evaluation. Conclusion Mammographic films presented higher values for maximum optical density and contrast resolution as compared with general purpose films. The utilized digital processing technique could only change the image pixels matrix values and did not affect the printing standard. The proposed digital image standard allows greater control of the relationship between pixels values and optical density obtained in the analysis of films quality and printing systems.

Color ad spectral image assessment using novel quality and fidelity techniques

The ongoing development of the digital media has brought a new set of challenges with it. As images containing more than three wavelength bands, often called spectral images, are becoming a more integral part of everyday life, problems in the quality of the RGB reproduction from the spectral images have turned into an important area of research. The notion of image quality is often thought to comprise two distinctive areas – image quality itself and image fidelity, both dealing with similar questions, image quality being the degree of excellence of the image, and image fidelity the measure of the match of the image under study to the original. In this thesis, both image fidelity and image quality are considered, with an emphasis on the influence of color and spectral image features on both. There are very few works dedicated to the quality and fidelity of spectral images. Several novel image fidelity measures were developed in this study, which include kernel similarity measures and 3D-SSIM (structural similarity index). The kernel measures incorporate the polynomial, Gaussian radial basis function (RBF) and sigmoid kernels. The 3D-SSIM is an extension of a traditional gray-scale SSIM measure developed to incorporate spectral data. The novel image quality model presented in this study is based on the assumption that the statistical parameters of the spectra of an image influence the overall appearance. The spectral image quality model comprises three parameters of quality: colorfulness, vividness and naturalness. The quality prediction is done by modeling the preference function expressed in JNDs (just noticeable difference). Both image fidelity measures and the image quality model have proven to be effective in the respective experiments.

Neural Network based studies on Spectroscopic Analysis and Image Processing

International School of Photonics, Cochin University of Science and Technology

Development of a Fully Automated Image Analysis Method for High Density cDNA and array CGH Microarray Based Genomic Studies

In this thesis, different techniques for image analysis of high density microarrays have been investigated. Most of the existing image analysis techniques require prior knowledge of image specific parameters and direct user intervention for microarray image quantification. The objective of this research work was to develop of a fully automated image analysis method capable of accurately quantifying the intensity information from high density microarrays images. The method should be robust against noise and contaminations that commonly occur in different stages of microarray development.

An entropy-based approach to automatic image segmentation of satellite images

An entropy-based image segmentation approach is introduced and applied to color images obtained from Google Earth. Segmentation refers to the process of partitioning a digital image in order to locate different objects and regions of interest. The application to satellite images paves the way to automated monitoring of ecological catastrophes, urban growth, agricultural activity, maritime pollution, climate changing and general surveillance. Regions representing aquatic, rural and urban areas are identified and the accuracy of the proposed segmentation methodology is evaluated. The comparison with gray level images revealed that the color information is fundamental to obtain an accurate segmentation. (C) 2010 Elsevier B.V. All rights reserved.

A Contour-based Separation of VerticallyAttached Traffic Signs

This report presents an algorithm for locating the cut points for and separatingvertically attached traffic signs in Sweden. This algorithm provides severaladvanced digital image processing features: binary image which representsvisual object and its complex rectangle background with number one and zerorespectively, improved cross correlation which shows the similarity of 2Dobjects and filters traffic sign candidates, simplified shape decompositionwhich smoothes contour of visual object iteratively in order to reduce whitenoises, flipping point detection which locates black noises candidates, chasmfilling algorithm which eliminates black noises, determines the final cut pointsand separates originally attached traffic signs into individual ones. At each step,the mediate results as well as the efficiency in practice would be presented toshow the advantages and disadvantages of the developed algorithm. Thisreport concentrates on contour-based recognition of Swedish traffic signs. Thegeneral shapes cover upward triangle, downward triangle, circle, rectangle andoctagon. At last, a demonstration program would be presented to show howthe algorithm works in real-time environment.

Análise digital de imagem e estereologia da angiogênese em adenomas e no adenocarcinoma colorretal invasivo de submucosa

A angiogênese é essencial no desenvolvimento neoplásico, associando-se às metástases à distância e recorrência em diversas neoplasias malignas. Em carcinomas colorretais, os parâmetros da análise digital de imagem e estereologia da angiogênese foram pouco estudados. Objetivo: avaliar parâmetros tridimensionais e a quantificação microvascular bidimensional nas diferentes apresentações morfológicas dos adenomas colorretais e no adenocarcinoma colorretal restrito à submucosa, a fim de determinar o papel da angiogênese nas diferentes etapas da seqüência adenoma-carcinoma e sua relação com as diferentes apresentações das lesões precursoras do carcinoma colorretal. Material e métodos: foi realizado estudo histórico de delineamento transversal, incluindo 115 lesões neoplásicas colorretais, ressecadas endoscópica ou cirurgicamente no período de 1997 a 2001, obtidas de pacientes do Hospital de Clínicas de Porto Alegre e da Fundação Universitária de Gastroenterologia (FUGAST). Para análise da angiogênese foram utilizadas as técnicas de imuno-histoquímica, análise digital de imagem, quantificação microvascular e estereologia. Os resultados foram apresentados como mediana e intervalos interquartis. Resultados: a quantificação microvascular foi progressivamente mais elevada nas lesões polipóides com displasia de alto grau comparadas às de baixo grau. Quanto maior o grau de atipia observado, maior foi o número de microvasos (regressão linear, P < 0,05). O volume e extensão microvascular foram diferentes entre as fases evolutivas da neoplasia colorretal, resultando em aumento no volume 728 (416 - 1408) versus 178 (93 - 601) e extensão microvascular 242,4 (131,1 - 936,8) vs 24,0 (6,5 - 142,2) (P < 0,001) nas lesões polipóides com displasia de alto grau comparadas às de baixo grau, respectivamente. A quantificação microvascular foi progressivamente mais elevada, acompanhando a progressão neoplásica polipóide: displasia de baixo grau 41,8 (15,8 - 71,9), displasia de alto grau 60,0 (23,0 - 95,6) e carcinoma de submucosa 76,0 (37,5 - 132,6) (P < 0,001). Concomitante, o volume 956 (436 - 2188) vs 178 (93 - 601) e a extensão microvascular 534,6 (146,7 - 1262) vs 24,0 (6,5 - 142,2) foram mais elevados nos adenocarcinomas colorretais restritos à submucosa em relação às lesões polipóides com displasia de baixo grau, respectivamente (P < 0,001). Não foi encontrada diferença estatisticamente significativa na angiogênese entre os adenomas polipóides e não-polipóides através da quantificação 41,8 (15,8 - 71,9) vs 22 (16 - 40) e estimativa da extensão microvascular 24 (6,5-142,2) vs 17,5 (4,4-54,7), respectivamente. Conclusão: a utilização da análise digital de imagem e estereologia acrescentou maior objetividade e eficácia na metodologia de avaliação angiogênica, pois permitiu a precisa segmentação das áreas hipervasculares, a representação da morfologia tridimensional característica do suprimento vascular e a identificação de diferenças na microvascularização nas etapas evolutivas do câncer colorretal.

Grapevine root distribution in drip and microsprinkler irrigation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Uso de índices de reflectância das folhas para avaliar o nível de nitrogênio em grama-bermuda

A reflectância da folha em determinados comprimentos de onda pode ser uma alternativa para estimar a concentração de nitrogênio (N) na planta, devido à relação entre o teor de clorofila e de N no tecido foliar. Este trabalho teve por objetivo avaliar índices da cor verde em grama-bermuda para predizer o nível de N na planta. O experimento foi conduzido em área comercial de produção de grama-bermuda, localizada na cidade de Capela do Alto/SP. O delineamento experimental utilizado foi de blocos ao acaso, com cinco tratamentos (0, 150, 300, 450 e 600kg de N ha-1) e quatro repetições. Foi avaliada a reflectância das folhas pelo uso de medidor de cor de grama, clorofilômetro, e por meio de análise da imagem digital. O matiz (H) e índice de cor verde escuro (ICVE), calculados com base nos índices de reflectância da imagem digital, o ICVE, obtido com medidor de cor de grama, e a intensidade de coloração verde (ICV), obtida com o clorofilômetro, apresentaram forte correlação positiva com a concentração de N e a taxa de cobertura do solo (TCS) da grama-bermuda, podendo ser utilizados como índices auxiliares na recomendação de adubação nitrogenada para a cultura. Os valores obtidos que podem servir como primeiros índices para avaliação do estado nutricional em N na grama-bermuda Celebration são: H de 88 a 109o e ICVE de 0,54 a 0,66 (imagem digital); H de 67 a 76o e ICVE de 0,41 a 0,44 (medidor de cor da grama TCM 500); e ICV de 374 a 471 (clorofilômetro CM 1000).

COMPARATIVE EVALUATION of OCULOMETRIC VARIABLES IN GRAVES' OPHTHALMOPATHY

OBJECTIVES: To estimate oculometric parameters of Graves' ophthalmopathy in comparison to healthy eyes using digital photography and digital image analysis.INTRODUCTION: Graves' ophthalmopathy is the main cause of eye proptosis. Because these protrusions cause clinically perceived distortions in orbital architecture, digital photographs can be used to detect and quantify these changes.METHODS: We carried out a cross-sectional study comprising 12 healthy volunteers and 15 Graves' ophthalmopathy patients with the purpose of evaluating the use of simple, non-invasive digital photography to estimate oculometric parameters of Graves' ophthalmopathy and compare them with the parameters of unaffected eyes. Facial photographs of cases and controls were taken in a standardized manner. Oculometric parameters were compared between the groups and then correlated to proptometer measures.RESULTS: All estimated oculometric variables showed significant differences between the groups, in particular with regard to mediopupilar aperture, lateral height, distance from the iris edge to the lateral boundary of the palpebral fissure, and distance from the higher point of the iris to the lateral limit of the palpebral fissure. The product of medial aperture and horizontal palpebral fissure also revealed greater discrepancy between the groups. Proptometer measures showed significant linear correlation between the distance from the iris edge to the lateral boundary of the palpebral fissure and between the distance from the higher point of the iris to the lateral limit of palpebral fissure (p<0.05).CONCLUSIONS: Comparative analysis of oculometric parameters in Graves' ophthalmopathy suggests that eye proptosis is related to an asymmetric increase in lateral oculometric measures. Standardized digital photographs can be used in clinical practice to objectively estimate oculometric parameters of Graves' ophthalmopathy patients.

Monitoramento geoambiental do estuário do Rio Paraíba do Norte - PB por meio da cartografia temática digital e de produtos de sensoriamento remoto

The North Paraíba River Estuary, located in the eastern portion of the Paraíba State, Northeast Brazil, on coordinates 34º50 00 -34º57 30 S and 6º55 00 -7º7 30 W, constitutes a fluvio-marine plain formed by the North Paraíba River and its tributaries Sanhauá, Paroeira, Mandacaru, Tiriri, Tambiá, Ribeira and Guia. This estuary comprises an area of about 260 km2. Increasing human demands on the estuary area and inadequate environment managing have generated conflicts. The present work main purpose is to evaluate the geodynamic evolution of the North Paraíba River Estuary in the period from 1969 to 2001, using digital image processing techniques, thematic digital cartography and multitemporal data integration, combined to geological-geophysical field surveys. The SUDENE cartographic database, converted to digital format were, used to obtain occupation and topographic maps from 1969 and to generate a Digital Elevation Model (DEM). Digital Landsat 7 ETM+ and Spot HRVIR-PAN satellite images interpretation allowed the environmental characterization of the estuary. The most important digital processing results were achieved color composites RGB 5-4-3, 5-3-1, 5-2-NDWI and band ratio 7/4-5/3-4/2, 5/7-3/1-5/4). In addition the fusion image technique RGBI was used by the inclusion of the Spot HRVRI and Landsat 7 ETM+ panchromatic band on I layer with RGB triplets 5-4-3, 5-3-1 and 5/7-3/1-5/4. The DEM and digital images integration allowed the identification of seven geomorphological units: coastal tableland, flowing tray, tide plain, fluvial terrace, submerged dune, beach plain and beach). Both Side Scan Sonar and Echosound were used to analyse underwater surface and bedforms of the estuarine channel, sand predominance (fine to very fine) and 2D dune features 5 m wide and 0.5 m height. This investigation characterized the estuary as an environment dominated by regimen of average flow. The channel depth varies between 1 m and 11 m, being this last quota reached in the area of Porto de Cabedelo. The chanel estuary is relatively shallow, with erosion evidences mainly on its superior portion, attested by sand banks exposed during the low tide. Multitemporal digital maps from 1969 and 2001 integration were obtained through geoprocessing techniques, resulting the geodynamic evolution of the estuary based on landuse, DEM geomorphology and bathymetric maps

Comparison of simulated periodontal bone defect depth measured in digital radiographs in dedicated and non-dedicated software systems

Objectives: To compare simulated periodontal bone defect depth measured in digital radiographs with dedicated and non-dedicated software systems and to compare the depth measurements from each program with the measurements in dry mandibles.Methods: Forty periodontal bone defects were created at the proximal area of the first premolar in dry pig mandibles. Measurements of the defects were performed with a periodontal probe in the dry mandible. Periapical digital radiographs of the defects were recorded using the Schick sensor in a standardized exposure setting. All images were read using a Schick dedicated software system (CDR DICOM for Windows v.3.5), and three commonly available non-dedicated software systems (Vix Win 2000 v.1.2; Adobe Photoshop 7.0 and Image Tool 3.0). The defects were measured three times in each image and a consensus was reached among three examiners using the four software systems. The difference between the radiographic measurements was analysed using analysis of variance (ANOVA) and by comparing the measurements from each software system with the dry mandibles measurements using Student's t-test.Results: the mean values of the bone defects measured in the radiographs were 5.07 rum, 5.06 rum, 5.01 mm and 5.11 mm for CDR Digital Image and Communication in Medicine (DICOM) for Windows, Vix Win, Adobe Photoshop, and Image Tool, respectively, and 6.67 mm for the dry mandible. The means of the measurements performed in the four software systems were not significantly different, ANOVA (P = 0.958). A significant underestimation of defect depth was obtained when we compared the mean depths from each software system with the dry mandible measurements (t-test; P congruent to 0.000).Conclusions: the periodontal bone defect measurements in dedicated and in three non-dedicated software systems were not significantly different, but they all underestimated the measurements when compared with the measurements obtained in the dry mandibles.

An image analysis study of pit formation on Ti-6Al-4V

Metallographic techniques and digital image processing have been used to investigate heat-treated Ti-6Al-4V pitting corrosion, often used as aircraft components. LM and SEM metallography of 'as received', annealed (heating up to 800 degreesC/30 min and cooling furnace) and aged (heating up to 900 degreesC/30 min, quenching in water, heating up to 540 degreesC/240 min and again water-quenched) microstructures reveal pitting sites at primary and secondary alpha/beta interfaces. Microstructural arrangements influence and corrosive environment association on pit morphology could be demonstrated by digital image analysis and results statistical treatment. (C) 2002 Elsevier B.V. B.V. All rights reserved.