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Jesus  Salido
  • Spain

Jesus Salido

Esta nueva versión surge de los comentarios de realimentación recibidos por los usuarios de esta y un proceso natural de evolución de este proyecto. Cada poco tiempo descubro algo nuevo que puedo modificar y que, en mi opinión, mejora el... more
Esta nueva versión surge de los comentarios de realimentación recibidos por los usuarios de esta y un proceso natural de evolución de este proyecto. Cada poco tiempo descubro algo nuevo que puedo modificar y que, en mi opinión, mejora el resultado final o la experiencia del usuario. En esta nueva release de la plantilla he decidido incluir bastantes cambios para facilitar su uso y configuración.
Autofocus evaluation for brightfield microscopy pathology
Autofocus evaluation for brightfield microscopy pathology
Currently, microalgae (i.e., diatoms) constitute a generally accepted bioindicator of water quality and therefore provide an index of the status of biological ecosystems. Diatom detection for specimen counting and sample classification... more
Currently, microalgae (i.e., diatoms) constitute a generally accepted bioindicator of water quality and therefore provide an index of the status of biological ecosystems. Diatom detection for specimen counting and sample classification are two difficult time-consuming tasks for the few existing expert diatomists. To mitigate this challenge, in this work, we propose a fully operative low-cost automated microscope, integrating algorithms for: (1) stage and focus control, (2) image acquisition (slide scanning, stitching, contrast enhancement), and (3) diatom detection and a prospective specimen classification (among 80 taxa). Deep learning algorithms have been applied to overcome the difficult selection of image descriptors imposed by classical machine learning strategies. With respect to the mentioned strategies, the best results were obtained by deep neural networks with a maximum precision of 86% (with the YOLO network) for detection and 99.51% for classification, among 80 different...
Given that angiogenesis and lymphangiogenesis are strongly related to prognosis in neoplastic and other pathologies and that many methods exist that provide different results, we aim to construct a morphometric tool allowing us to measure... more
Given that angiogenesis and lymphangiogenesis are strongly related to prognosis in neoplastic and other pathologies and that many methods exist that provide different results, we aim to construct a morphometric tool allowing us to measure different aspects of the shape and size of vascular vessels in a complete and accurate way. The developed tool presented is based on vessel closing which is an essential property to properly characterize the size and the shape of vascular and lymphatic vessels. The method is fast and accurate improving existing tools for angiogenesis analysis. The tool also improves the accuracy of vascular density measurements, since the set of endothelial cells forming a vessel is considered as a single object.
Diatom identification is a crucial process to estimate water quality, which is essential in biological studies. This process can be automated with machine learning algorithms. For this purpose, a dataset with 10 common taxa is collected,... more
Diatom identification is a crucial process to estimate water quality, which is essential in biological studies. This process can be automated with machine learning algorithms. For this purpose, a dataset with 10 common taxa is collected, with annotations provided by an expert diatomist. In this work, a comparison of the classical state-of-the-art general purpose methods along with two different deep learning approaches is carried out. The classical methods are based on Viola-Jones and scale and curvature invariant ridge object detectors. The deep learning based methods are Semantic Segmentation and YOLO. This is the first time that Viola-Jones and Semantic Segmentation techniques are applied and compared for diatom segmentation in microscopic images containing several taxon shells. While all methods provide relatively good results in specific species, the deep learning approaches are consistently better in terms of sensitivity and specificity (up to 0.99 for some taxa) and up to 0.8...
There is a great need to implement preventive mechanisms against shootings and terrorist acts in public spaces with a large influx of people. While surveillance cameras have become common, the need for monitoring 24/7 and real-time... more
There is a great need to implement preventive mechanisms against shootings and terrorist acts in public spaces with a large influx of people. While surveillance cameras have become common, the need for monitoring 24/7 and real-time response requires automatic detection methods. This paper presents a study based on three convolutional neural network (CNN) models applied to the automatic detection of handguns in video surveillance images. It aims to investigate the reduction of false positives by including pose information associated with the way the handguns are held in the images belonging to the training dataset. The results highlighted the best average precision (96.36%) and recall (97.23%) obtained by RetinaNet fine-tuned with the unfrozen ResNet-50 backbone and the best precision (96.23%) and F1 score values (93.36%) obtained by YOLOv3 when it was trained on the dataset including pose information. This last architecture was the only one that showed a consistent improvement—aroun...
Deep learning (henceforth DL) has become most powerful machine learning methodology. Under specific circumstances recognition rates even surpass those obtained by humans. Despite this, several works have shown that deep learning produces... more
Deep learning (henceforth DL) has become most powerful machine learning methodology. Under specific circumstances recognition rates even surpass those obtained by humans. Despite this, several works have shown that deep learning produces outputs that are very far from human responses when confronted with the same task. This the case of the so-called “adversarial examples” (henceforth AE). The fact that such implausible misclassifications exist points to a fundamental difference between machine and human learning. This paper focuses on the possible causes of this intriguing phenomenon. We first argue that the error in adversarial examples is caused by high bias, i.e. by regularization that has local negative effects. This idea is supported by our experiments in which the robustness to adversarial examples is measured with respect to the level of fitting to training samples. Higher fitting was associated to higher robustness to adversarial examples. This ties the phenomenon to the tra...
Currently, microalgae (i.e., diatoms) constitute a generally accepted bioindicator of water quality and therefore provide an index of the status of biological ecosystems. Diatom detection for specimen counting and sample classification... more
Currently, microalgae (i.e., diatoms) constitute a generally accepted bioindicator of water quality and therefore provide an index of the status of biological ecosystems. Diatom detection for specimen counting and sample classification are two difficult time-consuming tasks for the few existing expert diatomists. To mitigate this challenge, in this work, we propose a fully operative low-cost automated microscope, integrating algorithms for: (1) stage and focus control, (2) image acquisition (slide scanning, stitching, contrast enhancement), and (3) diatom detection and a prospective specimen classification (among 80 taxa). Deep learning algorithms have been applied to overcome the difficult selection of image descriptors imposed by classical machine learning strategies. With respect to the mentioned strategies, the best results were obtained by deep neural networks with a maximum precision of 86{\%} (with the YOLO network) for detection and 99.51{\%} for classification, among 80 dif...
Diatom identification is a crucial process to estimate water quality, which is essential in biological studies. This process can be automated with machine learning algorithms. For this purpose, a dataset with 10 common taxa is collected,... more
Diatom identification is a crucial process to estimate water quality, which is essential in biological studies. This process can be automated with machine learning algorithms. For this purpose, a dataset with 10 common taxa is collected, with annotations provided by an expert diatomist. In this work, a comparison of the classical state-of-the-art general purpose methods along with two different deep learning approaches is carried out. The classical methods are based on Viola-Jones and scale and curvature invariant ridge object detectors. The deep learning based methods are Semantic Segmentation and YOLO. This is the first time that Viola-Jones and Semantic Segmentation techniques are applied and compared for diatom segmentation in microscopic images containing several taxon shells. While all methods provide relatively good results in specific species, the deep learning approaches are consistently better in terms of sensitivity and specificity (up to 0.99 for some taxa) and up to 0.86 precision.
An essential and indispensable component of automated microscopy framework is the automatic focus-ing system, which determines the in-focus position of a given field of view by searching the maximum value of a focusing function over a... more
An essential and indispensable component of automated microscopy framework is the automatic focus-ing system, which determines the in-focus position of a given field of view by searching the maximum value of a focusing function over a range of z-axis positions. The focus function and its computation time are crucial to the accuracy and efficiency of the system. Sixteen focusing algorithms were analyzed for histological and histopatho-logical images. In terms of accuracy, results have shown an overall high performance by most of the methods. However, we included in the evaluation study other criteria such as computational cost and focusing curve shape which are crucial for real-time applications and were used to highlight the best practices.
Several studies have established a relationship between the preoperative hemoglobin level and the need for postoperative blood transfusion. We analyzed the relationship between preoperative hemoglobin levels, as well as other factors such... more
Several studies have established a relationship between the preoperative hemoglobin level and the need for postoperative blood transfusion. We analyzed the relationship between preoperative hemoglobin levels, as well as other factors such as age, gender, weight, height, type and duration of the total joint replacement surgery, and the need for postoperative blood transfusion. A retrospective study of 296 patients treated with 370 procedures (209 total hip arthroplasties [56.5%] and 161 total knee arthroplasties [43.5%]) from 1994 to 1998 was carried out. A univariate analysis was performed to establish the relationship between all independent variables and the need for postoperative transfusion. Variables that were determined to have a significant relationship were included in a multivariate analysis. The univariate analysis revealed a significant relationship between the need for postoperative blood transfusion and preoperative hemoglobin levels (p = 0.0001), duration of surgery (p = 0.0001), weight (p = 0.002), height (p = 0.019), and gender (p = 0.0056). However, the multivariate analysis identified a significant relationship only between the need for transfusion and the preoperative hemoglobin level (p = 0.0001) and weight (p = 0.011); height (p = 0.776) and gender (p = 0.122) were discounted as significant factors. Patients with a preoperative hemoglobin level of <130 g/L had a four times greater risk of having a transfusion than did those with a hemoglobin level between 130 and 150 g/L and a 15.3 times greater risk than did those with a hemoglobin level of >150 g/L. The preoperative hemoglobin level (p = 0.0001) and weight of the patient (p = 0.011) were shown to predict the need for blood transfusion after hip and knee replacement.
Breast cancer diagnosis is still done by observation of biopsies under the microscope. The development of automated methods for breast TMA classification would reduce diagnostic time. This paper is a step towards the solution for this... more
Breast cancer diagnosis is still done by observation of biopsies under the microscope. The development of automated methods for breast TMA classification would reduce diagnostic time. This paper is a step towards the solution for this problem and shows a complete study of breast TMA classification based on colour models and texture descriptors. The TMA images were divided into four classes: i) benign stromal tissue with cellularity, ii) adipose tissue, iii) benign and benign anomalous structures, and iv) ductal and lobular carcinomas. A relevant set of features was obtained on eight different colour models from first and second order Haralick statistical descriptors obtained from the intensity image, Fourier, Wavelets, Multiresolution Gabor, M-LBP and textons descriptors. Furthermore, four types of classification experiments were performed using six different classifiers: (1) classification per colour model individually, (2) classification by combination of colour models, (3) classi...
Deals with the optimization of the reactive navigation performed with fuzzy behaviors in partially known environments. It offers the integration of the fuzzy behaviors with global path-planning techniques in a nested hierarchical... more
Deals with the optimization of the reactive navigation performed with fuzzy behaviors in partially known environments. It offers the integration of the fuzzy behaviors with global path-planning techniques in a nested hierarchical architecture for autonomous vehicle navigation. A three level architecture is proposed based on a global path-planner level, a fuzzy behaviors level and an execution level. While the global
Breast cancer is the most common type of cancer and the fifth leading cause of death in women over 40. Therefore, prompt diagnostic and treatment is essential. In this work a TMA Computer Aided Diagnosis (CAD) system has been implemented... more
Breast cancer is the most common type of cancer and the fifth leading cause of death in women over 40. Therefore, prompt diagnostic and treatment is essential. In this work a TMA Computer Aided Diagnosis (CAD) system has been implemented to provide support to pathologists in their daily work. For that purpose, the tool covers each and every process from the TMA core image acquisition to their individual classification. The first process includes: tissue core location, segmentation and rigid registration of digital microscopic images acquired at different magnifications (5x, 10x, 20x, 20x and 40x) from different devices. The classification process allows performing the core classification selecting different types of color models, texture descriptors and classifiers. Finally, the cores are classified into three categories: malignant, doubtful and benign.
Contenido: 1) Introducción; 2) Conceptos básicos de robótica; 3) Sistemas de locomoción de robots; 4) Hardware de control; 5) Control de robots móviles; 6) Programación de robots móviles; 7) Sistemas sensoriales; 8) Dispositivos de... more
Contenido: 1) Introducción; 2) Conceptos básicos de robótica; 3) Sistemas de locomoción de robots; 4) Hardware de control; 5) Control de robots móviles; 6) Programación de robots móviles; 7) Sistemas sensoriales; 8) Dispositivos de actuación; 9) Sistemas mecánicos de transmisión de potencia; 10) Alimentación eléctrica de sistemas autónomos.
Grid technology has enabled clustering and access to, and interaction among, a wide variety of geographically distributed resources such as supercomputers, storage systems, data sources, instruments as well as special devices and... more
Grid technology has enabled clustering and access to, and interaction among, a wide variety of geographically distributed resources such as supercomputers, storage systems, data sources, instruments as well as special devices and services, realizing network-centric operations. Their main applications include large scale computational and data intensive problems in science and engineering. Grids are likely to have a deep impact on health related applications. Moreover, they seem to be suitable for tissue-based diagnosis. They offer a powerful tool to deal with current challenges in many biomedical domains involving complex anatomical and physiological modeling of structures from images or large image databases assembling and analysis. This chapter analyzes the general structures and functions of a Grid environment implemented for tissue-based diagnosis on digital images. Moreover, it presents a Grid middleware implemented by the authors for diagnostic pathology applications. The chap...
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This paper describes a specific tool for automatically segmenting and archiving of tissue microarray (TMA) cores in microscopy images at different magnifications. TMA enables researchers to extract the small cylinders of a single tissue... more
This paper describes a specific tool for automatically segmenting and archiving of tissue microarray (TMA) cores in microscopy images at different magnifications. TMA enables researchers to extract the small cylinders of a single tissue (core sections) from histological sections and arrange them in an array on a paraffin block such that hundreds can be analyzed simultaneously. A crucial step to improve the speed and quality of this process is the correct localization of each tissue core in the array. However, usually the tissue cores are not aligned in the microarray, the TMA cores are incomplete and the images are noisy and with distorted colors. We develop a robust framework to handle core sections under these conditions. The algorithms are able to detect, stitch, and archive the TMA cores at different magnifications. Once the TMA cores are segmented they are stored in a relational database allowing their processing for further studies of benign-malignant classification. The method was shown to be reliable for handling the TMA cores and therefore enabling further large-scale molecular pathology research.
... atribuidas a los laboratorios remotos potenciadas aún más en un campus distribuido geográficamente como ... ya que ahora la ejecución del programa principal de control es distribuida entre el ... acceso remoto se puede realizar bien... more
... atribuidas a los laboratorios remotos potenciadas aún más en un campus distribuido geográficamente como ... ya que ahora la ejecución del programa principal de control es distribuida entre el ... acceso remoto se puede realizar bien desde los mismos puestos de laboratorio en el ...
The field of anatomic pathology has experienced major changes over the last decade. Virtual microscopy (VM) systems have allowed experts in pathology and other biomedical areas to work in a safer and more collaborative way. VMs are... more
The field of anatomic pathology has experienced major changes over the last decade. Virtual microscopy (VM) systems have allowed experts in pathology and other biomedical areas to work in a safer and more collaborative way. VMs are automated systems capable of digitizing microscopic samples that were traditionally examined one by one. The possibility of having digital copies reduces the risk of damaging original samples, and also makes it easier to distribute copies among other pathologists. This article describes the development of an automated high-resolution whole slide imaging (WSI) system tailored to the needs and problems encountered in digital imaging for pathology, from hardware control to the full digitization of samples. The system has been built with an additional digital monochromatic camera together with the color camera by default and LED transmitted illumination (RGB). Monochrome cameras are the preferred method of acquisition for fluorescence microscopy. The system is able to digitize correctly and form large high resolution microscope images for both brightfield and fluorescence. The quality of the digital images has been quantified using three metrics based on sharpness, contrast and focus. It has been proved on 150 tissue samples of brain autopsies, prostate biopsies and lung cytologies, at five magnifications: 2.5×, 10×, 20×, 40×, and 63×. The article is focused on the hardware set-up and the acquisition software, although results of the implemented image processing techniques included in the software and applied to the different tissue samples are also presented.
Page 1. 273 13 Microscopic Imaging Gloria Bueno, Oscar Déniz, Roberto González-Morales, Juan Vidal, and Jesús Salido 13.1 Introduction Microscopic imaging provides invaluable research support for important fields such ...
Delayed wound healing after total arthroplasty puts the patient at risk for superficial and deep infection, with substantial economic and social consequences. The objective of this study was to assess serum zinc levels as a tool for... more
Delayed wound healing after total arthroplasty puts the patient at risk for superficial and deep infection, with substantial economic and social consequences. The objective of this study was to assess serum zinc levels as a tool for predicting such a delay in patients with primary osteoarthritis or osteoarthritis secondary to avascular necrosis. We conducted a prospective study of 80 total hip arthroplasties, analyzing possible correlations between delayed healing and serum zinc, nutritional parameters, and other demographic and epidemiological variables. The predictive value of preoperative serum zinc levels and lymphocyte counts was confirmed; thus, an arthroplasty procedure could be timed to minimize risk.
After emergency fasciotomy in acute compartment syndrome, skin graft techniques are usually necessary to cover the wound. The shoelace technique for gradual skin closure was retrospectively analyzed after having been applied in 20... more
After emergency fasciotomy in acute compartment syndrome, skin graft techniques are usually necessary to cover the wound. The shoelace technique for gradual skin closure was retrospectively analyzed after having been applied in 20 patients with acute compartment syndrome. With the application of this technique, none of the cases required new surgical interventions to close the wound. Closure was reached in an average time of 8.8 days, with an average hospital stay of 10 days and a low rate of complications. Gradual skin closure using the shoelace technique avoids the use of free skin grafts to close the dermotomy-fasciotomy wounds, reducing the need for anesthesia, nursing care, and hospital stays of patients, resulting in lower healthcare costs.

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