Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids.
In oncology, two-dimensional in-vitro culture models are the standard test beds for the discovery and development of cancer treatments, but in the last decades, evidence emerged that such models have low predictive value for clinical efficacy. Therefore they are increasingly complemented by more phy...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4909318?pdf=render |
| _version_ | 1818241841630281728 |
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| author | Michaël Barbier Steffen Jaensch Frans Cornelissen Suzana Vidic Kjersti Gjerde Ronald de Hoogt Ralph Graeser Emmanuel Gustin Yolanda T Chong IMI PREDECT Consortium |
| author_facet | Michaël Barbier Steffen Jaensch Frans Cornelissen Suzana Vidic Kjersti Gjerde Ronald de Hoogt Ralph Graeser Emmanuel Gustin Yolanda T Chong IMI PREDECT Consortium |
| author_sort | Michaël Barbier |
| collection | DOAJ |
| description | In oncology, two-dimensional in-vitro culture models are the standard test beds for the discovery and development of cancer treatments, but in the last decades, evidence emerged that such models have low predictive value for clinical efficacy. Therefore they are increasingly complemented by more physiologically relevant 3D models, such as spheroid micro-tumor cultures. If suitable fluorescent labels are applied, confocal 3D image stacks can characterize the structure of such volumetric cultures and, for example, cell proliferation. However, several issues hamper accurate analysis. In particular, signal attenuation within the tissue of the spheroids prevents the acquisition of a complete image for spheroids over 100 micrometers in diameter. And quantitative analysis of large 3D image data sets is challenging, creating a need for methods which can be applied to large-scale experiments and account for impeding factors. We present a robust, computationally inexpensive 2.5D method for the segmentation of spheroid cultures and for counting proliferating cells within them. The spheroids are assumed to be approximately ellipsoid in shape. They are identified from information present in the Maximum Intensity Projection (MIP) and the corresponding height view, also known as Z-buffer. It alerts the user when potential bias-introducing factors cannot be compensated for and includes a compensation for signal attenuation. |
| first_indexed | 2024-12-12T13:35:45Z |
| format | Article |
| id | doaj.art-d6adf23124fc40dca32e5c00a44812b3 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T13:35:45Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-d6adf23124fc40dca32e5c00a44812b32022-12-22T00:22:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01116e015694210.1371/journal.pone.0156942Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids.Michaël BarbierSteffen JaenschFrans CornelissenSuzana VidicKjersti GjerdeRonald de HoogtRalph GraeserEmmanuel GustinYolanda T ChongIMI PREDECT ConsortiumIn oncology, two-dimensional in-vitro culture models are the standard test beds for the discovery and development of cancer treatments, but in the last decades, evidence emerged that such models have low predictive value for clinical efficacy. Therefore they are increasingly complemented by more physiologically relevant 3D models, such as spheroid micro-tumor cultures. If suitable fluorescent labels are applied, confocal 3D image stacks can characterize the structure of such volumetric cultures and, for example, cell proliferation. However, several issues hamper accurate analysis. In particular, signal attenuation within the tissue of the spheroids prevents the acquisition of a complete image for spheroids over 100 micrometers in diameter. And quantitative analysis of large 3D image data sets is challenging, creating a need for methods which can be applied to large-scale experiments and account for impeding factors. We present a robust, computationally inexpensive 2.5D method for the segmentation of spheroid cultures and for counting proliferating cells within them. The spheroids are assumed to be approximately ellipsoid in shape. They are identified from information present in the Maximum Intensity Projection (MIP) and the corresponding height view, also known as Z-buffer. It alerts the user when potential bias-introducing factors cannot be compensated for and includes a compensation for signal attenuation.http://europepmc.org/articles/PMC4909318?pdf=render |
| spellingShingle | Michaël Barbier Steffen Jaensch Frans Cornelissen Suzana Vidic Kjersti Gjerde Ronald de Hoogt Ralph Graeser Emmanuel Gustin Yolanda T Chong IMI PREDECT Consortium Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids. PLoS ONE |
| title | Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids. |
| title_full | Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids. |
| title_fullStr | Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids. |
| title_full_unstemmed | Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids. |
| title_short | Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids. |
| title_sort | ellipsoid segmentation model for analyzing light attenuated 3d confocal image stacks of fluorescent multi cellular spheroids |
| url | http://europepmc.org/articles/PMC4909318?pdf=render |
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