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RNA expression analysis and quantification from images during limb regeneration
dc.contributor.advisor | Muñoz Romero, José Javier | |
dc.contributor.advisor | Comellas Sanfeliu, Ester | |
dc.contributor.author | Franky Vargas, Enrique | |
dc.date.accessioned | 2024-03-01T21:23:35Z | |
dc.date.available | 2024-03-01T21:23:35Z | |
dc.date.issued | 2023 | |
dc.identifier.uri | https://repositorio.escuelaing.edu.co/handle/001/2869 | |
dc.description | Collection of whole-mount images captured using light sheet fluorescence microscopy (LSFM), displaying the chemical signals within a regenerating axolotl forelimb. | eng |
dc.description.abstract | This work implements a fundamental methodology to analyze the expression of morphogens, which are molecules or factors that act as fundamental chemical signals in the development of an organism and are essential for the formation of patterns in biology. These morphogens are present in images obtained through LFSM (Light Sheet Fluorescence Microscopy) during the regeneration process of the synovial joint in Axolotls, captured using the HCR FISH technique (Fluorescent In Situ Hybridization Chain Reaction), with the aim of quantifying and measuring the main concentration patterns. To achieve this, the tools provided by image analysis applications in the MATLAB environment are used in conjunction with the theory related to fluorescence image analysis and the fundamentals of biological images. The main objective is to establish a reference framework for the proposed models in the prediction of Turing patterns in cellular regeneration. | eng |
dc.description.abstract | Este trabajo implementa una metodología para analizar la expresión de los morfogenes, que son moléculas o factores que actúan como señales químicas fundamentales en el desarrollo de un organismo, y son esenciales para la formación de patrones en la biología. Estos morfogenes están presentes en imágenes de LFSM (microscopía de lámina de fluorescencia por luz) obtenidas durante el proceso de regeneración de la articulación sinovial del Axolotl, capturadas mediante la técnica de HCR FISH (Cadena de Reacción de Hibridación Fluorescente in situ, por sus siglas en inglés), con el fin de cuantificar y medir los principales patrones de concentración. Para lograrlo, se utilizan las herramientas proporcionadas por las aplicaciones de análisis de imágenes en el entorno MATLAB, en conjunción con la teoría relacionada con el análisis de imágenes de fluorescencia y los fundamentos de las imágenes biológicas. El objetivo principal es establecer un marco de referencia para los modelos propuestos en la predicción de patrones de Turing en la regeneración celular. | spa |
dc.description.tableofcontents | INDEX RESUMEN ____________________________________________________________2 RESUM ______________________________________________________________3 ABSTRACT____________________________________________________________4 ACKNOWLEDGMENTS __________________________________________________6 PREFACE _____________________________________________________________9 Background..............................................................................................................................9 Motivation................................................................................................................................9 1. INTRODUCTION__________________________________________________11 2. OBJECTIVES _____________________________________________________14 3. METHODOLOGY _________________________________________________15 3.1. Preprocessing ..............................................................................................................16 3.1.1. Structure of images – Z stack.....................................................................................16 3.1.2. Uploading image information and metadata properties to MATLAB workspace. ......................................................................................................................................16 3.1.3. Pyramidal resolution ..................................................................................................20 3.1.4. Blur and point spread function. ................................................................................20 3.1.5. Background subtraction.............................................................................................23 3.1.6. Noise ............................................................................................................................24 3.2. Processing....................................................................................................................26 3.2.1. Histogram analysis......................................................................................................26 3.2.2. Binarization..................................................................................................................27 3.2.3. Morphological operation...........................................................................................29 3.2.4. Segmentation..............................................................................................................31 3.3. Post – processing ........................................................................................................33 3.3.1. Selection of parameters and segmented pattern...................................................33 3.3.2. Measure original properties......................................................................................33 4. RESULTS ________________________________________________________35 DISCUSSION _________________________________________________________39 Global reference....................................................................................................................39 Parametrization.....................................................................................................................40 Pág. 8 Memory 8 CONCLUSSIONS ______________________________________________________41 ECONOMIC ANALYSIS _________________________________________________42 AMBIENTAL IMPACT __________________________________________________43 BIBLIOGRAPHY _______________________________________________________45 ANNEX______________________________________________________________48 Results for different filter values.........................................................................................48 Day 14 post amputation ..........................................................................................................48 Day 15 post amputation ..........................................................................................................50 Day 17 post amputation ..........................................................................................................52 Day 18 post amputation ..........................................................................................................54 Day 21 post amputation ..........................................................................................................56 Day 26 post amputation ..........................................................................................................58 | eng |
dc.format.extent | 61 p. | spa |
dc.format.mimetype | application/pdf | spa |
dc.language.iso | eng | spa |
dc.publisher | Universidad Politécnica de Cataluña | spa |
dc.rights.uri | https://creativecommons.org/licenses/by-nc/4.0/ | spa |
dc.title | RNA expression analysis and quantification from images during limb regeneration | eng |
dc.type | Trabajo de grado - Pregrado | spa |
dc.type.version | info:eu-repo/semantics/publishedVersion | spa |
oaire.accessrights | http://purl.org/coar/access_right/c_abf2 | spa |
oaire.version | http://purl.org/coar/version/c_970fb48d4fbd8a85 | spa |
dc.description.degreelevel | Pregrado | spa |
dc.description.degreename | Ingeniero(a) Biomédico(a) | spa |
dc.identifier.url | https://catalogo-intra.escuelaing.edu.co/cgi-in/koha/cataloguing/additem.pl?biblionumber=23685 | |
dc.publisher.place | Bogotá | spa |
dc.publisher.program | Ingeniería Biomédica | spa |
dc.relation.indexed | N/A | spa |
dc.rights.accessrights | info:eu-repo/semantics/openAccess | spa |
dc.rights.creativecommons | Atribución-NoComercial 4.0 Internacional (CC BY-NC 4.0) | spa |
dc.subject.armarc | Morfogenésis | spa |
dc.subject.armarc | Embriología | spa |
dc.subject.armarc | Morfología (Biología) | spa |
dc.subject.armarc | Regeneración (Biología) | spa |
dc.subject.proposal | Limb regeneration | eng |
dc.subject.proposal | RNA pathways | eng |
dc.subject.proposal | Axolotl | eng |
dc.type.coar | http://purl.org/coar/resource_type/c_7a1f | spa |
dc.type.content | Text | spa |
dc.type.driver | info:eu-repo/semantics/bachelorThesis | spa |
dc.type.redcol | https://purl.org/redcol/resource_type/TP | spa |
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