RNA expression analysis and quantification from images during limb regeneration
Collection of whole-mount images captured using light sheet fluorescence microscopy (LSFM), displaying the chemical signals within a regenerating axolotl forelimb.
- Autores:
-
Franky Vargas, Enrique
- Tipo de recurso:
- Trabajo de grado de pregrado
- Fecha de publicación:
- 2023
- Institución:
- Escuela Colombiana de Ingeniería Julio Garavito
- Repositorio:
- Repositorio Institucional ECI
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.escuelaing.edu.co:001/2869
- Acceso en línea:
- https://repositorio.escuelaing.edu.co/handle/001/2869
https://catalogo-intra.escuelaing.edu.co/cgi-in/koha/cataloguing/additem.pl?biblionumber=23685
- Palabra clave:
- Morfogenésis
Embriología
Morfología (Biología)
Regeneración (Biología)
Limb regeneration
RNA pathways
Axolotl
- Rights
- openAccess
- License
- https://creativecommons.org/licenses/by-nc/4.0/
| id |
ESCUELAIG2_031531d6bc59cd1053b47a9403e93c49 |
|---|---|
| oai_identifier_str |
oai:repositorio.escuelaing.edu.co:001/2869 |
| network_acronym_str |
ESCUELAIG2 |
| network_name_str |
Repositorio Institucional ECI |
| repository_id_str |
|
| dc.title.eng.fl_str_mv |
RNA expression analysis and quantification from images during limb regeneration |
| title |
RNA expression analysis and quantification from images during limb regeneration |
| spellingShingle |
RNA expression analysis and quantification from images during limb regeneration Morfogenésis Embriología Morfología (Biología) Regeneración (Biología) Limb regeneration RNA pathways Axolotl |
| title_short |
RNA expression analysis and quantification from images during limb regeneration |
| title_full |
RNA expression analysis and quantification from images during limb regeneration |
| title_fullStr |
RNA expression analysis and quantification from images during limb regeneration |
| title_full_unstemmed |
RNA expression analysis and quantification from images during limb regeneration |
| title_sort |
RNA expression analysis and quantification from images during limb regeneration |
| dc.creator.fl_str_mv |
Franky Vargas, Enrique |
| dc.contributor.advisor.none.fl_str_mv |
Muñoz Romero, José Javier Comellas Sanfeliu, Ester |
| dc.contributor.author.none.fl_str_mv |
Franky Vargas, Enrique |
| dc.subject.armarc.spa.fl_str_mv |
Morfogenésis Embriología Morfología (Biología) Regeneración (Biología) |
| topic |
Morfogenésis Embriología Morfología (Biología) Regeneración (Biología) Limb regeneration RNA pathways Axolotl |
| dc.subject.proposal.eng.fl_str_mv |
Limb regeneration RNA pathways Axolotl |
| description |
Collection of whole-mount images captured using light sheet fluorescence microscopy (LSFM), displaying the chemical signals within a regenerating axolotl forelimb. |
| publishDate |
2023 |
| dc.date.issued.none.fl_str_mv |
2023 |
| dc.date.accessioned.none.fl_str_mv |
2024-03-01T21:23:35Z |
| dc.date.available.none.fl_str_mv |
2024-03-01T21:23:35Z |
| dc.type.spa.fl_str_mv |
Trabajo de grado - Pregrado |
| dc.type.coarversion.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.version.spa.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
| dc.type.coar.spa.fl_str_mv |
http://purl.org/coar/resource_type/c_7a1f |
| dc.type.content.spa.fl_str_mv |
Text |
| dc.type.driver.spa.fl_str_mv |
info:eu-repo/semantics/bachelorThesis |
| dc.type.redcol.spa.fl_str_mv |
https://purl.org/redcol/resource_type/TP |
| format |
http://purl.org/coar/resource_type/c_7a1f |
| status_str |
publishedVersion |
| dc.identifier.uri.none.fl_str_mv |
https://repositorio.escuelaing.edu.co/handle/001/2869 |
| dc.identifier.url.none.fl_str_mv |
https://catalogo-intra.escuelaing.edu.co/cgi-in/koha/cataloguing/additem.pl?biblionumber=23685 |
| url |
https://repositorio.escuelaing.edu.co/handle/001/2869 https://catalogo-intra.escuelaing.edu.co/cgi-in/koha/cataloguing/additem.pl?biblionumber=23685 |
| dc.language.iso.spa.fl_str_mv |
eng |
| language |
eng |
| dc.relation.indexed.spa.fl_str_mv |
N/A |
| dc.rights.coar.fl_str_mv |
http://purl.org/coar/access_right/c_abf2 |
| dc.rights.uri.spa.fl_str_mv |
https://creativecommons.org/licenses/by-nc/4.0/ |
| dc.rights.accessrights.spa.fl_str_mv |
info:eu-repo/semantics/openAccess |
| dc.rights.creativecommons.spa.fl_str_mv |
Atribución-NoComercial 4.0 Internacional (CC BY-NC 4.0) |
| rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc/4.0/ Atribución-NoComercial 4.0 Internacional (CC BY-NC 4.0) http://purl.org/coar/access_right/c_abf2 |
| eu_rights_str_mv |
openAccess |
| dc.format.extent.spa.fl_str_mv |
61 p. |
| dc.format.mimetype.spa.fl_str_mv |
application/pdf |
| dc.publisher.spa.fl_str_mv |
Universidad Politécnica de Cataluña |
| dc.publisher.place.spa.fl_str_mv |
Bogotá |
| dc.publisher.program.spa.fl_str_mv |
Ingeniería Biomédica |
| institution |
Escuela Colombiana de Ingeniería Julio Garavito |
| bitstream.url.fl_str_mv |
https://repositorio.escuelaing.edu.co/bitstream/001/2869/6/23-08-24__TFG%20Enrique%20Franky%20Vargas_rev_10.pdf.jpg https://repositorio.escuelaing.edu.co/bitstream/001/2869/8/Autorizaci%c3%b3n%20de%20publicaci%c3%b3nFranky.pdf.jpg https://repositorio.escuelaing.edu.co/bitstream/001/2869/5/23-08-24__TFG%20Enrique%20Franky%20Vargas_rev_10.pdf.txt https://repositorio.escuelaing.edu.co/bitstream/001/2869/7/Autorizaci%c3%b3n%20de%20publicaci%c3%b3nFranky.pdf.txt https://repositorio.escuelaing.edu.co/bitstream/001/2869/4/license.txt https://repositorio.escuelaing.edu.co/bitstream/001/2869/1/23-08-24__TFG%20Enrique%20Franky%20Vargas_rev_10.pdf https://repositorio.escuelaing.edu.co/bitstream/001/2869/3/Autorizaci%c3%b3n%20de%20publicaci%c3%b3nFranky.pdf |
| bitstream.checksum.fl_str_mv |
a299e1c3ad63e994e0dee9d8c0b344fc 5fe7834862cc6b25e8eb171e5917d837 d99570e3f47ca447db9a1f04b5c71df5 1bf51ef50dafd5baf383093399673683 5a7ca94c2e5326ee169f979d71d0f06e 579b3c18c54bb67583a59f577e3ca5c6 9cefad26ae134a61ae017280a849fcd7 |
| bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 MD5 MD5 MD5 MD5 MD5 |
| repository.name.fl_str_mv |
Repositorio Escuela Colombiana de Ingeniería Julio Garavito |
| repository.mail.fl_str_mv |
repositorio.eci@escuelaing.edu.co |
| _version_ |
1814355593714991104 |
| spelling |
Muñoz Romero, José Javier52c5576827a200f13a6237767c10526bComellas Sanfeliu, Ester2149e43db3b46e277af8cd7b94b18beeFranky Vargas, Enrique87d8e40195a50fe4dbd9ebfa3d2cb7ce2024-03-01T21:23:35Z2024-03-01T21:23:35Z2023https://repositorio.escuelaing.edu.co/handle/001/2869https://catalogo-intra.escuelaing.edu.co/cgi-in/koha/cataloguing/additem.pl?biblionumber=23685Collection of whole-mount images captured using light sheet fluorescence microscopy (LSFM), displaying the chemical signals within a regenerating axolotl forelimb.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.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.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 ..........................................................................................................58PregradoIngeniero(a) Biomédico(a)61 p.application/pdfengUniversidad Politécnica de CataluñaBogotáIngeniería Biomédicahttps://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessAtribución-NoComercial 4.0 Internacional (CC BY-NC 4.0)http://purl.org/coar/access_right/c_abf2RNA expression analysis and quantification from images during limb regenerationTrabajo de grado - Pregradoinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_7a1fTextinfo:eu-repo/semantics/bachelorThesishttps://purl.org/redcol/resource_type/TPhttp://purl.org/coar/version/c_970fb48d4fbd8a85N/AMorfogenésisEmbriologíaMorfología (Biología)Regeneración (Biología)Limb regenerationRNA pathwaysAxolotlTHUMBNAIL23-08-24__TFG Enrique Franky Vargas_rev_10.pdf.jpg23-08-24__TFG Enrique Franky Vargas_rev_10.pdf.jpgGenerated Thumbnailimage/jpeg9158https://repositorio.escuelaing.edu.co/bitstream/001/2869/6/23-08-24__TFG%20Enrique%20Franky%20Vargas_rev_10.pdf.jpga299e1c3ad63e994e0dee9d8c0b344fcMD56open accessAutorización de publicaciónFranky.pdf.jpgAutorización de publicaciónFranky.pdf.jpgGenerated Thumbnailimage/jpeg12810https://repositorio.escuelaing.edu.co/bitstream/001/2869/8/Autorizaci%c3%b3n%20de%20publicaci%c3%b3nFranky.pdf.jpg5fe7834862cc6b25e8eb171e5917d837MD58metadata only accessTEXT23-08-24__TFG Enrique Franky Vargas_rev_10.pdf.txt23-08-24__TFG Enrique Franky Vargas_rev_10.pdf.txtExtracted texttext/plain78574https://repositorio.escuelaing.edu.co/bitstream/001/2869/5/23-08-24__TFG%20Enrique%20Franky%20Vargas_rev_10.pdf.txtd99570e3f47ca447db9a1f04b5c71df5MD55open accessAutorización de publicaciónFranky.pdf.txtAutorización de publicaciónFranky.pdf.txtExtracted texttext/plain3430https://repositorio.escuelaing.edu.co/bitstream/001/2869/7/Autorizaci%c3%b3n%20de%20publicaci%c3%b3nFranky.pdf.txt1bf51ef50dafd5baf383093399673683MD57metadata only accessLICENSElicense.txtlicense.txttext/plain; charset=utf-81881https://repositorio.escuelaing.edu.co/bitstream/001/2869/4/license.txt5a7ca94c2e5326ee169f979d71d0f06eMD54open accessORIGINAL23-08-24__TFG Enrique Franky Vargas_rev_10.pdf23-08-24__TFG Enrique Franky Vargas_rev_10.pdfTesis finalapplication/pdf3984816https://repositorio.escuelaing.edu.co/bitstream/001/2869/1/23-08-24__TFG%20Enrique%20Franky%20Vargas_rev_10.pdf579b3c18c54bb67583a59f577e3ca5c6MD51open accessAutorización de publicaciónFranky.pdfAutorización de publicaciónFranky.pdfautorización de publicaciónapplication/pdf849510https://repositorio.escuelaing.edu.co/bitstream/001/2869/3/Autorizaci%c3%b3n%20de%20publicaci%c3%b3nFranky.pdf9cefad26ae134a61ae017280a849fcd7MD53metadata only access001/2869oai:repositorio.escuelaing.edu.co:001/28692024-03-04 16:17:31.155open accessRepositorio Escuela Colombiana de Ingeniería Julio Garavitorepositorio.eci@escuelaing.edu.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 |