Browsing by Author "Serranho, Pedro"
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- Adaptive complex diffusion noise despeckling for 3D OCT DataPublication . Bernardes, Rui; Maduro, Cristina; Serranho, Pedro; Dinis, João; Cunha-Vaz, JoséPurpose: To demonstrate the performance of a recently proposed despeckling filter when extended to 3D in OCT data. Methods: A new formulation for a complex diffusion filter was recently proposed [1] being adaptive in time and adjusting parameters to data, facilitating diffusion in the vitreous and reducing it in the retina to preserve tissue information. This new formulation outperformed, both quantitatively and qualitatively, currently existing filters, while at the same time was computationally more efficient attaining the same despeckling level in 34% of the computing time. We have now extended it to perform 3D OCT despeckling achieving a significant improvement in noise removal. We have resorted to a mathematical based synthetic OCT scan in order to assess quantitative results in 3D. In addition, we have applied this 3D filter to a set of 72 eye scans, from healthy volunteers (20), diabetic retinopathy (20), cystoid macular edema (2), age-related macular degeneration (20) and choroidal neo-vascularization (10), who underwent high-definition Cirrus OCT (Carl Zeiss Meditec, Dublin, CA, USA) using macular cube protocols (200x200x1024 and/or 512x128x1024). Results: The extension from 2D to 3D of this adaptive complex diffusion filter proved to be beneficial by achieving an increased level of noise reduction while simultaneously better preserving fundamental information. These facts are supported from well known metrics (e.g. MSE-mean squared error, ENL-effective number of looks and CNR-contrast-to-noise ratio) for the synthetic OCT scan and from the assessment made by 3 retina specialist who graded qualitatively the output of the 2D and 3D filters. Conclusions: These findings demonstrate this new formulation and its extension to 3D is beneficial for human analysis of OCT data and suggest it might be an important tool for automated data processing as in segmentation of retinal structures. [1] Bernardes R, Maduro C, Serranho P, Araújo A, Barbeiro S, Cunha-Vaz J. Improved adaptive complex diffusion despeckling filter. OPTICS EXPRESS 18(23):24048-24059, 2010.
- Bioestatística com SPSS: notas de apoioPublication . Serranho, Pedro; Ramos, Maria do RosárioNotas de apoio ao curso de "Biostestatística com SPSS" leccionado pelos Prof. Doutor Francisco Caramelo (Universidade de Coimbra), Prof. Doutora Maria Rosário Ramos e Prof. Doutor Pedro Serranho.
- Characterization of the retinal changes of the 3×Tg-AD mouse model of Alzheimer’s diseasePublication . Ferreira, Hugo; Martins, João; Nunes, Ana; Moreira, Paula I.; Castelo-Branco, Miguel; Ambrósio, António F.; Serranho, Pedro; Bernardes, RuiAlzheimer’s disease (AD) is a progressive neurodegenerative disorder whose diagnosis remains a notable challenge. The literature suggests that cerebral changes precede AD symptoms by over two decades, implying a significantly advanced stage of AD by the time it is usually diagnosed. In the study herein, texture analysis was applied to computed optical coherence tomography ocular fundus images to identify differences between a group of the transgenic mouse model of the Alzheimer’s disease (3×Tg-AD) and a group of wild-type mice, at the ages of one and two-months-old. A substantial difference between groups was found at both time-points across all neuroretina’s layers. Here, the inner nuclear layer stands out both in the level of statistically significant differences and on the extension of these differences which span through the imaged area. Also, the progression of AD is suggested to be spotted by texture analysis as demonstrated by the significant difference found in the inner plexiform and the outer nuclear layers from the age of one to the age of two-months-old. These findings demonstrate the potential of the use of the retina and texture analysis to the diagnosis of AD and monitor AD progression. Besides, the differences between groups found in this study suggest that the 3×Tg-AD model may be inappropriate to study early changes associated with the AD and other animal models should be tested following the same path and rationale. Moreover, these results also suggest that the human genes present in these transgenic mice may have an impact on the neurodevelopment of offspring which would justify the significant changes found at the age of one-month-old.
- Digital ocular fundus imaging: a reviewPublication . Bernardes, Rui; Serranho, Pedro; Lobo, ConceiçãoOcular fundus imaging plays a key role in monitoring the health status of the human eye. Currently, a large number of imaging modalities allow the assessment and/or quantification of ocular changes from a healthy status. This review focuses on the main digital fundus imaging modality, color fundus photography, with a brief overview of complementary techniques, such as fluorescein angiography. While focusing on two-dimensional color fundus photography, the authors address the evolution from nondigital to digital imaging and its impact on diagnosis. They also compare several studies performed along the transitional path of this technology. Retinal image processing and analysis, automated disease detection and identification of the stage of diabetic retinopathy (DR) are addressed as well. The authors emphasize the problems of image segmentation, focusing on the major landmark structures of the ocular fundus: the vascular network, optic disk and the fovea. Several proposed approaches for the automatic detection of signs of disease onset and progression, such as microaneurysms, are surveyed. A thorough comparison is conducted among different studies with regard to the number of eyes/subjects, imaging modality, fundus camera used, field of view and image resolution to identify the large variation in characteristics from one study to another. Similarly, the main features of the proposed classifications and algorithms for the automatic detection of DR are compared, thereby addressing computer-aided diagnosis and computer-aided detection for use in screening programs.
- Improved adaptive complex diffusion despeckling filterPublication . Bernardes, Rui; Maduro, Cristina; Serranho, Pedro; Araújo, Adérito; Barbeiro, Sílvia; Cunha-Vaz, JoséDespeckling optical coherence tomograms from the human retina is a fundamental step to a better diagnosis or as a preprocessing stage for retinal layer segmentation. Both of these applications are particularly important in monitoring the progression of retinal disorders. In this study we propose a new formulation for a well-known nonlinear complex diffusion filter. A regularization factor is now made to be dependent on data, and the process itself is now an adaptive one. Experimental results making use of synthetic data show the good performance of the proposed formulation by achieving better quantitative results and increasing computation speed.
- Improving the conditioning of the method of fundamental solutions for the Helmholtz equation on domains in polar or elliptic coordinatesPublication . Antunes, Pedro R. S.; Calunga, Hernani; Serranho, PedroA new approach to overcome the ill-conditioning of the Method of Fundamental Solutions (MFS) combining Singular Value Decomposition (SVD) and an adequate change of basis was introduced in [1] as MFS-SVD. The original formulation considered polar coordinates and harmonic polynomials as basis functions and is restricted to the Laplace equation in 2D. In this work, we start by adapting the approach to the Helmholtz equation in 2D and later extending it to elliptic coordinates. As in the Laplace case, the approach in polar coordinates has very good numerical results both in terms of conditioning and accuracy for domains close to a disk but does not perform so well for other domains, such as an eccentric ellipse. We therefore consider the MFS-SVD approach in elliptic coordinates with Mathieu functions as basis functions for the latter. We illustrate the feasibility of the approach by numerical examples in both cases.
- Inverse problems and medical imaging: lecture notesPublication . Serranho, PedroLecture notes for the curricular unit of Inverse Problems and Medical Imaging (23036 - https://guiadoscursos.uab.pt/en/ucs/problemas-inversos-e-imagiologia-medica/ ) of the Doctor’s Degree in Applied Mathematics and Modelling of Universidade Aberta.
- Lisbon young mathematicians conference 2023: book of abstractsPublication . Serranho, Pedro; Cipriano, Fernanda; Ferreira, Gilda; Gonçalves, Carlota; Grossinho, M. Rosário; Oliveira, M. Rosário; Ramos, Maria do RosárioBook of Abstracts of the Lisbon Young Mathematicians Conference 2023, held in Universidade Aberta at April 14-15, 2023
- Longitudinal normative OCT retinal thickness data for wild-type mice, and characterization of changes in the 3×Tg-AD mice model of Alzheimer's diseasePublication . Ferreira, Hugo; Martins, João; Moreira, Paula I.; Ambrósio, António F.; Castelo-Branco, Miguel; Serranho, Pedro; Bernardes, RuiMice are widely used as models for many diseases, including eye and neurodegenerative diseases. However, there is a lack of normative data for retinal thickness over time, especially at young ages. In this work, we present a normative thickness database from one to four-months-old, for nine layers/layer-aggregates, including the total retinal thickness, obtained from the segmentation of spectral-domain optical coherence tomography (SD-OCT) data from the C57BL6/129S mouse strain. Based on fifty-seven mice, this normative database provides an opportunity to study the ageing of control mice and characterize disease models' ageing, such as the triple transgenic mouse model of Alzheimer's disease (3×Tg-AD) used in this work. We report thickness measurements, the differences in thickness per layer, demonstrate a nasal-temporal asymmetry, and the variation of thickness as a function to the distance to the optic disc center. Significant differences were found between the transgenic group's thickness and the normative database for the entire period covered in this study. Even though it is well accepted that retinal nerve fiber layer (RNFL) thinning is a hallmark of neurodegeneration, our results show a thicker RNFL-GCL (RNFL-Ganglion cell layer) aggregate for the 3×Tg-AD mice until four-months-old.
- Noninvasive evaluation of retinal leakage using optical coherence tomographyPublication . Bernardes, Rui; Santos, Torcato; Serranho, Pedro; Lobo, Conceição; Cunha-Vaz, JoséPurpose: To demonstrate the association between changes in the blood-retinal barrier (BRB) identified by fluorescein leakage and those in the optical properties of the human retina determined by optical coherence tomography (OCT) and show how these changes can be quantified and their location identified within the retina. Methods: Two imaging techniques were applied: the retinal leakage analyzer, to map BRB function into intact or disrupted regions, and OCT, to measure refractive index changes along the light path within the human ocular fundus. Results: A total of 140 comparisons were made, 77 between areas of regions receiving the same classification (intact or disrupted BRB) and 63 between areas of regions receiving distinct classifications, from 4 pathological cases: 2 eyes with nonproliferative diabetic retinopathy and 2 eyes with wet age-related macular degeneration. In all cases, the distribution of OCT data between regions of intact and regions of disrupted BRB, identified by the retinal leakage analyzer, was quantified and was statistically significantly different (p < 0.001). In addition, it was found that the differences could be localized in the retina to specific structural sequences. Conclusions: Using a novel method to analyze OCT data, we showed that it may be possible to quantify differences in the extracellular compartment in eyes with retinal disease and alterations of the BRB. Based on quantitative techniques, our findings demonstrate the presence of indirect information on the BRB status within noninvasive OCT data.