Ground truth determination for segmentation of tomographic volumes using interpolation

Detalhes bibliográficos
Autor(a) principal: Rodolpho, Beatriz Leão
Data de Publicação: 2013
Tipo de documento: Dissertação
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/10832
Resumo: Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica
id RCAP_9ef6ac0bffac771324e0902ae3d5af8d
oai_identifier_str oai:run.unl.pt:10362/10832
network_acronym_str RCAP
network_name_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository_id_str 7160
spelling Ground truth determination for segmentation of tomographic volumes using interpolation3D segmentationGround truthComputed tomographyCancer3D interpolationSoftwareDissertação para obtenção do Grau de Mestre em Engenharia BiomédicaOptical projection tomographic microscopy allows for a 3D analysis of individual cells, making it possible to study its morphology. The 3D imagining technique used in this thesis uses white light excitation to image stained cells, and is referred to as single-cell optical computed tomography (cell CT). Studies have shown that morphological characteristics of the cell and its nucleus are deterministic in cancer diagnoses. For a more complete and accurate analysis of these characteristics, a fully-automated analysis of the single-cell 3D tomographic images can be done. The first step is segmenting the image into the different cell components. To assess how accurate the segmentation is, there is a need to determine ground truth of the automated segmentation. This dissertation intends to expose a method of obtaining ground truth for 3D segmentation of single cells. This was achieved by developing a software in CSharp. The software allows the user to input a visual segmentation of each 2D slice of a 3D volume by using a pen to trace the visually identified boundary of a cell component on a tablet. With this information, the software creates a segmentation of a 3D tomographic image that is a result of human visual segmentation. To increase the speed of this process, interpolation algorithms can be used. Since it is very time consuming to draw on every slice the user can skip slices. Interpolation algorithms are used to interpolate on the skipped slices. Five different interpolation algorithms were written: Linear Interpolation, Gaussian splat, Marching Cubes, Unorganized Points, and Delaunay Triangulation. To evaluate the performance of each interpolation algorithm the following evaluation metrics were used: Jaccard Similarity, Dice Coefficient, Specificity and Sensitivity.After evaluating each interpolation method we concluded that linear interpolation was the most accurate interpolation method, producing the best segmented volume for a faster ground truth determination method.Faculdade de Ciências e TecnologiaMeldrum, DeidreJohnson, RogerRUNRodolpho, Beatriz Leão2013-12-09T17:26:59Z20132013-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10362/10832TID:201762315enginfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T03:44:48Zoai:run.unl.pt:10362/10832Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:19:45.728327Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Ground truth determination for segmentation of tomographic volumes using interpolation
title Ground truth determination for segmentation of tomographic volumes using interpolation
spellingShingle Ground truth determination for segmentation of tomographic volumes using interpolation
Rodolpho, Beatriz Leão
3D segmentation
Ground truth
Computed tomography
Cancer
3D interpolation
Software
title_short Ground truth determination for segmentation of tomographic volumes using interpolation
title_full Ground truth determination for segmentation of tomographic volumes using interpolation
title_fullStr Ground truth determination for segmentation of tomographic volumes using interpolation
title_full_unstemmed Ground truth determination for segmentation of tomographic volumes using interpolation
title_sort Ground truth determination for segmentation of tomographic volumes using interpolation
author Rodolpho, Beatriz Leão
author_facet Rodolpho, Beatriz Leão
author_role author
dc.contributor.none.fl_str_mv Meldrum, Deidre
Johnson, Roger
RUN
dc.contributor.author.fl_str_mv Rodolpho, Beatriz Leão
dc.subject.por.fl_str_mv 3D segmentation
Ground truth
Computed tomography
Cancer
3D interpolation
Software
topic 3D segmentation
Ground truth
Computed tomography
Cancer
3D interpolation
Software
description Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica
publishDate 2013
dc.date.none.fl_str_mv 2013-12-09T17:26:59Z
2013
2013-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/10832
TID:201762315
url http://hdl.handle.net/10362/10832
identifier_str_mv TID:201762315
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Faculdade de Ciências e Tecnologia
publisher.none.fl_str_mv Faculdade de Ciências e Tecnologia
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799137840565583872

Registros relacionados