Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool
Abstract Background Efficient tools allowing the extraction of 2D surfaces from 3D-microscopy data are essential for studies aiming to decipher the complex cellular choreography through which epithelium morphogenesis takes place during development. Most existing methods allow for the extraction of a...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-08-01
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| Series: | BMC Biology |
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| Online Access: | https://doi.org/10.1186/s12915-022-01378-0 |
| _version_ | 1818082344076050432 |
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| author | Céline Trébeau Jacques Boutet de Monvel Gizem Altay Jean-Yves Tinevez Raphaël Etournay |
| author_facet | Céline Trébeau Jacques Boutet de Monvel Gizem Altay Jean-Yves Tinevez Raphaël Etournay |
| author_sort | Céline Trébeau |
| collection | DOAJ |
| description | Abstract Background Efficient tools allowing the extraction of 2D surfaces from 3D-microscopy data are essential for studies aiming to decipher the complex cellular choreography through which epithelium morphogenesis takes place during development. Most existing methods allow for the extraction of a single and smooth manifold of sufficiently high signal intensity and contrast, and usually fail when the surface of interest has a rough topography or when its localization is hampered by other surrounding structures of higher contrast. Multiple surface segmentation entails laborious manual annotations of the various surfaces separately. Results As automating this task is critical in studies involving tissue-tissue or tissue-matrix interaction, we developed the Zellige software, which allows the extraction of a non-prescribed number of surfaces of varying inclination, contrast, and texture from a 3D image. The tool requires the adjustment of a small set of control parameters, for which we provide an intuitive interface implemented as a Fiji plugin. Conclusions As a proof of principle of the versatility of Zellige, we demonstrate its performance and robustness on synthetic images and on four different types of biological samples, covering a wide range of biological contexts. |
| first_indexed | 2024-12-10T19:20:36Z |
| format | Article |
| id | doaj.art-26b02e3392e84459a0be11554a8fb9a3 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-12-10T19:20:36Z |
| publishDate | 2022-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-26b02e3392e84459a0be11554a8fb9a32022-12-22T01:36:29ZengBMCBMC Biology1741-70072022-08-0120111810.1186/s12915-022-01378-0Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software toolCéline Trébeau0Jacques Boutet de Monvel1Gizem Altay2Jean-Yves Tinevez3Raphaël Etournay4Institut Pasteur, Université Paris Cité, Inserm, Institut de l’AuditionInstitut Pasteur, Université Paris Cité, Inserm, Institut de l’AuditionInstitut Pasteur, Université Paris Cité, Inserm, Institut de l’AuditionInstitut Pasteur, Université Paris Cité, Image Analysis HubInstitut Pasteur, Université Paris Cité, Inserm, Institut de l’AuditionAbstract Background Efficient tools allowing the extraction of 2D surfaces from 3D-microscopy data are essential for studies aiming to decipher the complex cellular choreography through which epithelium morphogenesis takes place during development. Most existing methods allow for the extraction of a single and smooth manifold of sufficiently high signal intensity and contrast, and usually fail when the surface of interest has a rough topography or when its localization is hampered by other surrounding structures of higher contrast. Multiple surface segmentation entails laborious manual annotations of the various surfaces separately. Results As automating this task is critical in studies involving tissue-tissue or tissue-matrix interaction, we developed the Zellige software, which allows the extraction of a non-prescribed number of surfaces of varying inclination, contrast, and texture from a 3D image. The tool requires the adjustment of a small set of control parameters, for which we provide an intuitive interface implemented as a Fiji plugin. Conclusions As a proof of principle of the versatility of Zellige, we demonstrate its performance and robustness on synthetic images and on four different types of biological samples, covering a wide range of biological contexts.https://doi.org/10.1186/s12915-022-01378-0Image analysisMorphology3D imagingTissue imagingImage segmentationSurface extraction |
| spellingShingle | Céline Trébeau Jacques Boutet de Monvel Gizem Altay Jean-Yves Tinevez Raphaël Etournay Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool BMC Biology Image analysis Morphology 3D imaging Tissue imaging Image segmentation Surface extraction |
| title | Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool |
| title_full | Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool |
| title_fullStr | Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool |
| title_full_unstemmed | Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool |
| title_short | Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool |
| title_sort | extracting multiple surfaces from 3d microscopy images in complex biological tissues with the zellige software tool |
| topic | Image analysis Morphology 3D imaging Tissue imaging Image segmentation Surface extraction |
| url | https://doi.org/10.1186/s12915-022-01378-0 |
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