BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models.
BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0148379&type=printable |
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| _version_ | 1849723445242232832 |
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| author | Cemal Cagatay Bilgin Gerald Fontenay Qingsu Cheng Hang Chang Ju Han Bahram Parvin |
| author_facet | Cemal Cagatay Bilgin Gerald Fontenay Qingsu Cheng Hang Chang Ju Han Bahram Parvin |
| author_sort | Cemal Cagatay Bilgin |
| collection | DOAJ |
| description | BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation. |
| format | Article |
| id | doaj-art-149fe4fabfbb48b5821de4b9a20b38c6 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-149fe4fabfbb48b5821de4b9a20b38c62025-08-20T03:11:01ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01113e014837910.1371/journal.pone.0148379BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models.Cemal Cagatay BilginGerald FontenayQingsu ChengHang ChangJu HanBahram ParvinBioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0148379&type=printable |
| spellingShingle | Cemal Cagatay Bilgin Gerald Fontenay Qingsu Cheng Hang Chang Ju Han Bahram Parvin BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models. PLoS ONE |
| title | BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models. |
| title_full | BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models. |
| title_fullStr | BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models. |
| title_full_unstemmed | BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models. |
| title_short | BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models. |
| title_sort | biosig3d high content screening of three dimensional cell culture models |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0148379&type=printable |
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