STERapp: semiautomatic software for stereological analysis. Application in the estimation of fish fecundity

Postprin

The Analysis of Properties of Schlieren Color Images

AbstractContribution treats the topic of experimental analysis of statistical properties of intensity images of red, green, blue component and grey-scale representation of color image of visualized optically transparent polymeric foil by means of schlieren method. As the subject of the analysis were corrected intensity images of RGB components and grayscale representation of color image of visualized foil. Properties of mean value and standard deviation of color components intensity levels and grayscale images for selected samples of 5 types of polymeric foils were studied. The analysis shows effect of the choice of color component. Characteristics calculated from the intensity image of blue component color image proved the best properties. Such a fact can be used in the case of defectoscopy and the foil recognition by the use of methodology of processing and statistical analysis of images visualized optical transparent polymeric foils captured by the color cameras

CT Radiomics in Colorectal Cancer: Detection of KRAS Mutation Using Texture Analysis and Machine Learning

In this work, by using descriptive techniques, the characteristics of the texture of the CT (computed tomography) image of patients with colorectal cancer were extracted and, subsequently, classified in KRAS+ or KRAS-. This was accomplished by using different classifiers, such as Support Vector Machine (SVM), Grading Boosting Machine (GBM), Neural Networks (NNET), and Random Forest (RF). Texture analysis can provide a quantitative assessment of tumour heterogeneity by analysing both the distribution and relationship between the pixels in the image. The objective of this research is to demonstrate that CT-based Radiomics can predict the presence of mutation in the KRAS gene in colorectal cancer. This is a retrospective study, with 47 patients from the University Hospital, with a confirmatory pathological analysis of KRAS mutation. The highest accuracy and kappa achieved were 83% and 64.7%, respectively, with a sensitivity of 88.9% and a specificity of 75.0%, achieved by the NNET classifier using the texture feature vectors combining wavelet transform and Haralick coefficients. The fact of being able to identify the genetic expression of a tumour without having to perform either a biopsy or a genetic test is a great advantage, because it prevents invasive procedures that involve complications and may present biases in the sample. As well, it leads towards a more personalized and effective treatmentThis work has received financial support from the Xunta de Galicia (Centro singular de investigación de Galicia, accreditation 2020–2023) and the European Union (European Regional Development Fund—ERDF), Project MTM2016-76969-PS

Computer aided diagnosis algorithms for digital microscopy

Automatic analysis and information extraction from an image is still a highly chal- lenging research problem in the computer vision area, attempting to describe the image content with computational and mathematical techniques. Moreover the in- formation extracted from the image should be meaningful and as most discrimi- natory as possible, since it will be used to categorize its content according to the analysed problem. In the Medical Imaging domain this issue is even more felt because many important decisions that affect the patient care, depend on the use- fulness of the information extracted from the image. Manage medical image is even more complicated not only due to the importance of the problem, but also because it needs a fair amount of prior medical knowledge to be able to represent with data the visual information to which pathologist refer. Today medical decisions that impact patient care rely on the results of laboratory tests to a greater extent than ever before, due to the marked expansion in the number and complexity of offered tests. These developments promise to improve the care of patients, but the more increase the number and complexity of the tests, the more increases the possibility to misapply and misinterpret the test themselves, leading to inappropriate diagnosis and therapies. Moreover, with the increased number of tests also the amount of data to be analysed increases, forcing pathologists to devote much time to the analysis of the tests themselves rather than to patient care and the prescription of the right therapy, especially considering that most of the tests performed are just check up tests and most of the analysed samples come from healthy patients. Then, a quantitative evaluation of medical images is really essential to overcome uncertainty and subjectivity, but also to greatly reduce the amount of data and the timing for the analysis. In the last few years, many computer assisted diagno- sis systems have been developed, attempting to mimic pathologists by extracting features from the images. Image analysis involves complex algorithms to identify and characterize cells or tissues using image pattern recognition technology. This thesis addresses the main problems associated to the digital microscopy analysis in histology and haematology diagnosis, with the development of algorithms for the extraction of useful information from different digital images, but able to distinguish different biological structures in the images themselves. The proposed methods not only aim to improve the degree of accuracy of the analysis, and reducing time, if used as the only means of diagnoses, but also they can be used as intermediate tools for skimming the number of samples to be analysed directly from the pathologist, or as double check systems to verify the correct results of the automated facilities used today

Computer aided diagnosis algorithms for digital microscopy

Automatic analysis and information extraction from an image is still a highly chal- lenging research problem in the computer vision area, attempting to describe the image content with computational and mathematical techniques. Moreover the in- formation extracted from the image should be meaningful and as most discrimi- natory as possible, since it will be used to categorize its content according to the analysed problem. In the Medical Imaging domain this issue is even more felt because many important decisions that affect the patient care, depend on the use- fulness of the information extracted from the image. Manage medical image is even more complicated not only due to the importance of the problem, but also because it needs a fair amount of prior medical knowledge to be able to represent with data the visual information to which pathologist refer. Today medical decisions that impact patient care rely on the results of laboratory tests to a greater extent than ever before, due to the marked expansion in the number and complexity of offered tests. These developments promise to improve the care of patients, but the more increase the number and complexity of the tests, the more increases the possibility to misapply and misinterpret the test themselves, leading to inappropriate diagnosis and therapies. Moreover, with the increased number of tests also the amount of data to be analysed increases, forcing pathologists to devote much time to the analysis of the tests themselves rather than to patient care and the prescription of the right therapy, especially considering that most of the tests performed are just check up tests and most of the analysed samples come from healthy patients. Then, a quantitative evaluation of medical images is really essential to overcome uncertainty and subjectivity, but also to greatly reduce the amount of data and the timing for the analysis. In the last few years, many computer assisted diagno- sis systems have been developed, attempting to mimic pathologists by extracting features from the images. Image analysis involves complex algorithms to identify and characterize cells or tissues using image pattern recognition technology. This thesis addresses the main problems associated to the digital microscopy analysis in histology and haematology diagnosis, with the development of algorithms for the extraction of useful information from different digital images, but able to distinguish different biological structures in the images themselves. The proposed methods not only aim to improve the degree of accuracy of the analysis, and reducing time, if used as the only means of diagnoses, but also they can be used as intermediate tools for skimming the number of samples to be analysed directly from the pathologist, or as double check systems to verify the correct results of the automated facilities used today

Perfluorooctanoic acid exposure assessment on common carp liver through image and ultrastructural investigation

Perfluorooctanoic acid (PFOA) poses particular concern as an emerging pollutant in both surface and ground waters. Fish, as a natural inhabitant of these waters and being highly representative of vertebrates, represents an ideal animal model to assess the toxic effects of PFOA. Hereby, liver microscopic texture was comparatively evaluated in individuals of common carp subchronically exposed to PFOA using grayscale differential box counting, a fractal analysis method. Furthermore, liver cytoplasmic glycogen areas and ultrastructure were also evaluated and compared to the image analysis findings. Redundancy Analysis was performed to assess, in summary, how much the variation of fractal dimension and lacunarity was explained by the concentration of PFOA in liver, the mass of liver and the number of proliferating cell nuclear antigen (PCNA)-immunoreactive nuclei. Treatment group ordination was better determined by fractal dimension than lacunarity. Interestingly, a significant complexity increase was associated with the modification of liver microscopic texture due to PFOA exposure. This complexity increase was related to “cloudy swelling”, possibly representing a primarily adaptive strategy against PFOA challenge, rather than a slight, reversible form of degeneration as traditionally proposed. The occurrence of endoplasmic reticulum stress, unfolded protein reaction and hormetic response was proposed and discussed

Enhancing spatio-chromatic representation with more-than-three color coding for image description

The extraction of spatio-chromatic features from color images is usually performed independently on each color channel. Usual 3D color spaces, such as RGB, present a high inter-channel correlation for natural images. This correlation can be reduced using color-opponent representations, but the spatial structure of regions with small color differences is not fully captured in two generic Red-Green and Blue-Yellow channels. To overcome these problems, we propose new color coding that is adapted to the specific content of each image. Our proposal is based on two steps: (a) setting the number of channels to the number of distinctive colors we find in each image (avoiding the problem of channel correlation), and (b) building a channel representation that maximizes contrast differences within each color channel (avoiding the problem of low local contrast). We call this approach more-than-three color coding (MTT) to emphasize the fact that the number of channels is adapted to the image content. The higher the color complexity of an image, the more channels can be used to represent it. Here we select distinctive colors as the most predominant in the image, which we call color pivots, and we build the new color coding strategy using these color pivots as a basis. To evaluate the proposed approach, we measure the efficiency in an image categorization task. We show how a generic descriptor improves performance at the description level when applied to the MTT coding

Automatic marbling prediction of sliced dry-cured ham using image segmentation, texture analysis and regression

Dry-cured ham is a traditional Mediterranean meat product consumed throughout the world. This product is very variable in terms of composition and quality. Consumer’s acceptability of this product is influenced by different factors, in particular, visual intramuscular fat and its distribution across the slice, also known as marbling. On-line marbling assessment is of great interest for the industry for classification purposes. However, until now this assessment has been traditionally carried out by panels of experts and this methodology cannot be implement in industry. We propose a complete automatic system to predict marbling degree of dry-cured ham slices, which combines: (1) the color texture features of regions of interest (ROIs) extracted automatically for each muscle; and (2) machine learning models to predict the marbling. For the ROIs extraction algorithm more than the 90% of pixels of the ROI fall into the true muscle. The proposed system achieves a correlation of 0.92 using the support vector regression and a set of color texture features including statistics of each channel of RGB color image and Haralick’s coefficients of its gray-level version. The mean absolute error was 0.46, which is lower than the standard desviation (0.5) of the marbling scores evaluated by experts. This high accuracy in the marbling prediction for sliced dry-cured ham would allow to deploy its application in the dry-cured ham industryThis work has received financial support from the Xunta de Galicia (Centro singular de investigación de Galicia, accreditation 2020– 2023) and the European Union (European Regional Development Fund–ERDF), Project ED431G-2019/04. IRTA’s contribution was also funded by the CCLabel project (RTI-2018- 096883-R-C41) and the CERCA programme from Generalitat de CatalunyaS

Handbook of Pathogens and Diseases in Cephalopods

The aim of this open access book is to facilitate the identification and description of the different organs as well as pathogens and diseases affecting the most representative species of cephalopods focussed on Sepia officinalis, Loligo vulgaris and Octopus vulgaris. These species are valuable ‘morphotype’ models and belong to the taxonomic groups Sepioidea, Myopsida and Octopoda, which include most of the species with a high market value and aquaculture potential. The study is based on photographs at macroscopic and histological level in order to illustrate the role of the most important pathogens and related diseases from the view of a pathological diagnosis. The reader is able to familiarize with functional anatomy, necropsy and general histology of adults and paralarvae, as well as with the identification of different pathogens and pathologies. This work is thus an invaluable guide for the diagnosis of cephalopod diseases. Besides including pathogens for non-European cephalopod species, it also provides a useful contribution encouraging marine pathologists, parasitologists, veterinarians and those involved in fishery sanitary assessments, aquarium maintenance and aquaculture practices aiming to increase their knowledge about the pathology of cephalopods

Evaluation of PD-L1 expression in various formalin-fixed paraffin embedded tumour tissue samples using SP263, SP142 and QR1 antibody clones

Background & objectives: Cancer cells can avoid immune destruction through the inhibitory ligand PD-L1. PD-1 is a surface cell receptor, part of the immunoglobulin family. Its ligand PD-L1 is expressed by tumour cells and stromal tumour infltrating lymphocytes (TIL). Methods: Forty-four cancer cases were included in this study (24 triple-negative breast cancers (TNBC), 10 non-small cell lung cancer (NSCLC) and 10 malignant melanoma cases). Three clones of monoclonal primary antibodies were compared: QR1 (Quartett), SP 142 and SP263 (Ventana). For visualization, ultraView Universal DAB Detection Kit from Ventana was used on an automated platform for immunohistochemical staining Ventana BenchMark GX. Results: Comparing the sensitivity of two different clones on same tissue samples from TNBC, we found that the QR1 clone gave higher percentage of positive cells than clone SP142, but there was no statistically significant difference. Comparing the sensitivity of two different clones on same tissue samples from malignant melanoma, the SP263 clone gave higher percentage of positive cells than the QR1 clone, but again the difference was not statistically significant. Comparing the sensitivity of two different clones on same tissue samples from NSCLC, we found higher percentage of positive cells using the QR1 clone in comparison with the SP142 clone, but once again, the difference was not statistically significant. Conclusion: The three different antibody clones from two manufacturers Ventana and Quartett, gave comparable results with no statistically significant difference in staining intensity/ percentage of positive tumour and/or immune cells. Therefore, different PD-L1 clones from different manufacturers can potentially be used to evaluate the PD- L1 status in different tumour tissues. Due to the serious implications of the PD-L1 analysis in further treatment decisions for cancer patients, every antibody clone, staining protocol and evaluation process should be carefully and meticulously validated