2018 IEEE Global Engineering Education Conference (EDUCON), 2018
Due to the changes created by the Bologna Accord, future engineers must learn not only how to mod... more Due to the changes created by the Bologna Accord, future engineers must learn not only how to model processes, but also how to analyse events and situations using mathematical tools. Even though problem solving is unanimously considered an important part of their education, sometimes students feel that the problems they are requested to solve are not related to those of the real world, making difficult for them to envision how they will apply their mathematical knowledge in their future working life. As part of a European project proposal, and in order to remove that psychological barrier, we have started to implement a new methodology in our Statistics classes, so students can benefit from a learning model better adapted to their professional needs. In this contribution, we describe the initial steps of a project whose goal is to teach the subject of Statistics in a more practice way, using real data to enable our students to achieve the competencies set for this matter in an easier way better adapted to the current times.
— The analysis of dot blot (macroarray) images is currently based on the human identification of ... more — The analysis of dot blot (macroarray) images is currently based on the human identification of positive/negative dots, which is a subjective and time consuming process. This paper presents a system for the automatic analysis of dot blot images, using a pre-defined grid of markers, including a number of ON and OFF controls. The geometric deformations of the input image are corrected, and the individual markers detected, both tasks fully automatically. Based on a previous training stage, the probability for each marker to be ON is established. This information is provided together with quality parameters for training, noise and classification, allowing for a fully automatic evaluation of a dot blot image. I.
Abstract—This paper presents a system for the automatic processing of Digital Images obtained fro... more Abstract—This paper presents a system for the automatic processing of Digital Images obtained from Gel Electrophoresis. The system identifies automatically the number and the location of lanes in the digital image, as well as the location of bands on each lane, without any intervention from the user. A reference lane with a know substance is used to compute the molecular weight of the observed (unknown) bands. The system performance was tested using 12 images, obtained from 4 gels with 3 different exposures. A total of 5443 bands were tested in 12 images, 672 reference / observed lane pairs. The average error in the estimation of molecular weight of 9.2%. I.
ABSTRACT Linear Algebra is one of the mathematical fields taught in the first year of university ... more ABSTRACT Linear Algebra is one of the mathematical fields taught in the first year of university study. In this paper, I describe the efforts to change the student's interest and motivation in Linear Algebra classes. I present some activities using Image Processing to ...
The increasing development of computer technologies has given rise to educational alternatives, f... more The increasing development of computer technologies has given rise to educational alternatives, facilitating the creation of new forms of learning in an attractive and motivating way. Teachers develop efforts to create learning techniques using methods that can facilitate the learning in different areas of knowledge. The purpose of this experiment is to describe a case study that the author made with first year students of Electromechanical and Mechanics Engineering in a Linear Algebra course at the Coimbra Institute of Engineering. The study involved the application of Digital Image Processing to teaching and learning the basic concepts of Linear Algebra. The experience was very enriching for the author as a teacher, as well as for the students, because it let them awaken the motivation to learn, the interest and taste for Linear Algebra.
In beef, the marbling flecks are determinant regarding to flavor and tenderness. Beef cuts with h... more In beef, the marbling flecks are determinant regarding to flavor and tenderness. Beef cuts with higher levels of marbling are likely to be tenderer, flavor full and juicier than cuts with lower marbling levels [1]. Therefore, the USDA (United States Department of Agriculture) quality grade standards are based on subjective evaluation of the relative degree of visible intramuscular fat [2]. There are 10 official marbling classes: devoid (D) practically devoid (PD), traces (TR), slight (SL), small (SM), modest (MT), moderate (MD) slightly abundant (SA), moderately abundant (MA) and abundant (AB). So, there is a growing interest in developing methods and techniques for beef quality classification using digital images. This paper presents an automatic methodology, based on image processing techniques, to identify and to locate the beef in the image and to calculate the marbling measures, in order to evaluate the beef quality. The tests realized showed that it is possible to use image an...
Abstract—Labeled molecular markers are an important tool in molecular biology. This work presents... more Abstract—Labeled molecular markers are an important tool in molecular biology. This work presents a method for the automatic identification of molecular markers in dot blot images. The method detects the location of markers in the image and their size. An experiment was made with 6 test images, which were used to produce an additional set of 222 images with various rotation, translation, contrast and noise levels. Over 7500 markers were identified automatically and compared with reference values obtained manually. The RMS error for the marker positioning in the original test images were between 1.1 and 3.8 pixels, which is about 1/10 of the typical radius (26 pixels). The method proposed was found to be almost insensitive to grid rotation and translation, and reasonably robust to image contrast changes and presence of noise. I.
ABSTRACT Ralstonia solanacearum (Rs) is a quarantine phytopathogenic bacterium accountable for he... more ABSTRACT Ralstonia solanacearum (Rs) is a quarantine phytopathogenic bacterium accountable for heavy economic losses worldwide. Monitoring and eradication programs required for this pathogen are dependent on the availability of time- and cost-efficient detection and typing methods. However, members of the Rs species complex are characterized by a high phenotypic and genetic diversity, which requires improved diagnostics methods.The currently available full genome sequences of several Rs strains allow for the selection of novel specific DNA markers using comparative genomics tools. In this work, seventeen novel markers were selected based on Rs-specific protein domains and thoroughly validated for specificity and stability, both in silico and using “wet lab” assays. PCR- and hybridization-based validation assays revealed that the DNA regions selected as markers were unevenly distributed amongst the tested strains, with nine markers present throughout the species complex. The distribution of the remaining eight markers was highly variable between the different analyzed strains and allowed to obtain strain-specific dot blot hybridization patterns particularly informative for typing. The average probability value of each strain being positive for each of the seventeen markers was calculated by an algorithm and used to obtain a dendrogram representing the hierarchical clustering analysis of Rs, according to the similarity of their hybridization patterns. We believe that this method can be a robust contribution for the straightforward genotyping of members from the Rs species complex. Furthermore, this quantitative hybridization approach would allow to construct databases increasingly informative to determine new Rs genotypes and infer epidemiological patterns.This article is protected by copyright. All rights reserved.
Proceedings - 4th International Congress on Image and Signal Processing, CISP 2011, 2011
ABSTRACT Counting the number of Collembola in digital images is a routine task in laboratories of... more ABSTRACT Counting the number of Collembola in digital images is a routine task in laboratories of soil ecotoxicology. This process is based on a direct visual identification of Collembola, and is consequently a time consuming task. This paper present a fully automatic system for counting the number of Collembola in digital images. The system selects the interest area of the image, detects and removes the specular reflection of the incident light, as well as the foam developed during laboratory experiment and finally identifies and counts the number of Collembola. The system performance was tested using 5 treatments with 9 or 10 replicates and 13 treatments with 4 or 5 replicates. A total of 111 images were tested and the results were compared with those obtained by manual identification. The average relative error between automatic and manual counts from multiple observations of the same treatment was 2:1%, which can be considered a good result, given that this value is below the standard deviation between multiple replicate counts.
This paper presents a method (GEIAS) for the automatic processing of digital images obtained from... more This paper presents a method (GEIAS) for the automatic processing of digital images obtained from Gel Electrophoresis. The performance of GEIAS was tested using 12 images, obtained from 4 gels with 3 different exposures with a total of 1082 bands, comparing the results provided by GEIAS and 3 other software tools. The GEIAS is able to fully automatically detect DNA
Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2010
The analysis of dot blot (macroarray) images is currently based on the human identification of po... more The analysis of dot blot (macroarray) images is currently based on the human identification of positive/negative dots, which is a subjective and time consuming process. This paper presents a system for the automatic analysis of dot blot images, using a pre-defined grid of markers, including a number of ON and OFF controls. The geometric deformations of the input image are
2018 IEEE Global Engineering Education Conference (EDUCON), 2018
Due to the changes created by the Bologna Accord, future engineers must learn not only how to mod... more Due to the changes created by the Bologna Accord, future engineers must learn not only how to model processes, but also how to analyse events and situations using mathematical tools. Even though problem solving is unanimously considered an important part of their education, sometimes students feel that the problems they are requested to solve are not related to those of the real world, making difficult for them to envision how they will apply their mathematical knowledge in their future working life. As part of a European project proposal, and in order to remove that psychological barrier, we have started to implement a new methodology in our Statistics classes, so students can benefit from a learning model better adapted to their professional needs. In this contribution, we describe the initial steps of a project whose goal is to teach the subject of Statistics in a more practice way, using real data to enable our students to achieve the competencies set for this matter in an easier way better adapted to the current times.
— The analysis of dot blot (macroarray) images is currently based on the human identification of ... more — The analysis of dot blot (macroarray) images is currently based on the human identification of positive/negative dots, which is a subjective and time consuming process. This paper presents a system for the automatic analysis of dot blot images, using a pre-defined grid of markers, including a number of ON and OFF controls. The geometric deformations of the input image are corrected, and the individual markers detected, both tasks fully automatically. Based on a previous training stage, the probability for each marker to be ON is established. This information is provided together with quality parameters for training, noise and classification, allowing for a fully automatic evaluation of a dot blot image. I.
Abstract—This paper presents a system for the automatic processing of Digital Images obtained fro... more Abstract—This paper presents a system for the automatic processing of Digital Images obtained from Gel Electrophoresis. The system identifies automatically the number and the location of lanes in the digital image, as well as the location of bands on each lane, without any intervention from the user. A reference lane with a know substance is used to compute the molecular weight of the observed (unknown) bands. The system performance was tested using 12 images, obtained from 4 gels with 3 different exposures. A total of 5443 bands were tested in 12 images, 672 reference / observed lane pairs. The average error in the estimation of molecular weight of 9.2%. I.
ABSTRACT Linear Algebra is one of the mathematical fields taught in the first year of university ... more ABSTRACT Linear Algebra is one of the mathematical fields taught in the first year of university study. In this paper, I describe the efforts to change the student's interest and motivation in Linear Algebra classes. I present some activities using Image Processing to ...
The increasing development of computer technologies has given rise to educational alternatives, f... more The increasing development of computer technologies has given rise to educational alternatives, facilitating the creation of new forms of learning in an attractive and motivating way. Teachers develop efforts to create learning techniques using methods that can facilitate the learning in different areas of knowledge. The purpose of this experiment is to describe a case study that the author made with first year students of Electromechanical and Mechanics Engineering in a Linear Algebra course at the Coimbra Institute of Engineering. The study involved the application of Digital Image Processing to teaching and learning the basic concepts of Linear Algebra. The experience was very enriching for the author as a teacher, as well as for the students, because it let them awaken the motivation to learn, the interest and taste for Linear Algebra.
In beef, the marbling flecks are determinant regarding to flavor and tenderness. Beef cuts with h... more In beef, the marbling flecks are determinant regarding to flavor and tenderness. Beef cuts with higher levels of marbling are likely to be tenderer, flavor full and juicier than cuts with lower marbling levels [1]. Therefore, the USDA (United States Department of Agriculture) quality grade standards are based on subjective evaluation of the relative degree of visible intramuscular fat [2]. There are 10 official marbling classes: devoid (D) practically devoid (PD), traces (TR), slight (SL), small (SM), modest (MT), moderate (MD) slightly abundant (SA), moderately abundant (MA) and abundant (AB). So, there is a growing interest in developing methods and techniques for beef quality classification using digital images. This paper presents an automatic methodology, based on image processing techniques, to identify and to locate the beef in the image and to calculate the marbling measures, in order to evaluate the beef quality. The tests realized showed that it is possible to use image an...
Abstract—Labeled molecular markers are an important tool in molecular biology. This work presents... more Abstract—Labeled molecular markers are an important tool in molecular biology. This work presents a method for the automatic identification of molecular markers in dot blot images. The method detects the location of markers in the image and their size. An experiment was made with 6 test images, which were used to produce an additional set of 222 images with various rotation, translation, contrast and noise levels. Over 7500 markers were identified automatically and compared with reference values obtained manually. The RMS error for the marker positioning in the original test images were between 1.1 and 3.8 pixels, which is about 1/10 of the typical radius (26 pixels). The method proposed was found to be almost insensitive to grid rotation and translation, and reasonably robust to image contrast changes and presence of noise. I.
ABSTRACT Ralstonia solanacearum (Rs) is a quarantine phytopathogenic bacterium accountable for he... more ABSTRACT Ralstonia solanacearum (Rs) is a quarantine phytopathogenic bacterium accountable for heavy economic losses worldwide. Monitoring and eradication programs required for this pathogen are dependent on the availability of time- and cost-efficient detection and typing methods. However, members of the Rs species complex are characterized by a high phenotypic and genetic diversity, which requires improved diagnostics methods.The currently available full genome sequences of several Rs strains allow for the selection of novel specific DNA markers using comparative genomics tools. In this work, seventeen novel markers were selected based on Rs-specific protein domains and thoroughly validated for specificity and stability, both in silico and using “wet lab” assays. PCR- and hybridization-based validation assays revealed that the DNA regions selected as markers were unevenly distributed amongst the tested strains, with nine markers present throughout the species complex. The distribution of the remaining eight markers was highly variable between the different analyzed strains and allowed to obtain strain-specific dot blot hybridization patterns particularly informative for typing. The average probability value of each strain being positive for each of the seventeen markers was calculated by an algorithm and used to obtain a dendrogram representing the hierarchical clustering analysis of Rs, according to the similarity of their hybridization patterns. We believe that this method can be a robust contribution for the straightforward genotyping of members from the Rs species complex. Furthermore, this quantitative hybridization approach would allow to construct databases increasingly informative to determine new Rs genotypes and infer epidemiological patterns.This article is protected by copyright. All rights reserved.
Proceedings - 4th International Congress on Image and Signal Processing, CISP 2011, 2011
ABSTRACT Counting the number of Collembola in digital images is a routine task in laboratories of... more ABSTRACT Counting the number of Collembola in digital images is a routine task in laboratories of soil ecotoxicology. This process is based on a direct visual identification of Collembola, and is consequently a time consuming task. This paper present a fully automatic system for counting the number of Collembola in digital images. The system selects the interest area of the image, detects and removes the specular reflection of the incident light, as well as the foam developed during laboratory experiment and finally identifies and counts the number of Collembola. The system performance was tested using 5 treatments with 9 or 10 replicates and 13 treatments with 4 or 5 replicates. A total of 111 images were tested and the results were compared with those obtained by manual identification. The average relative error between automatic and manual counts from multiple observations of the same treatment was 2:1%, which can be considered a good result, given that this value is below the standard deviation between multiple replicate counts.
This paper presents a method (GEIAS) for the automatic processing of digital images obtained from... more This paper presents a method (GEIAS) for the automatic processing of digital images obtained from Gel Electrophoresis. The performance of GEIAS was tested using 12 images, obtained from 4 gels with 3 different exposures with a total of 1082 bands, comparing the results provided by GEIAS and 3 other software tools. The GEIAS is able to fully automatically detect DNA
Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2010
The analysis of dot blot (macroarray) images is currently based on the human identification of po... more The analysis of dot blot (macroarray) images is currently based on the human identification of positive/negative dots, which is a subjective and time consuming process. This paper presents a system for the automatic analysis of dot blot images, using a pre-defined grid of markers, including a number of ON and OFF controls. The geometric deformations of the input image are
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