title: BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models.
abstract: 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.
authors.affiliation: Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Cemal Cagatay
authors.initials: CC
authors.lastname: Bilgin
authors.affiliation: Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Gerald
authors.initials: G
authors.lastname: Fontenay
authors.affiliation: University of Nevada, Reno, Department of Electrical and Biomedical Engineering, Reno, NV, United States of America.|Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Qingsu
authors.initials: Q
authors.lastname: Cheng
authors.affiliation: University of Nevada, Reno, Department of Electrical and Biomedical Engineering, Reno, NV, United States of America.|Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Hang
authors.initials: H
authors.lastname: Chang
authors.affiliation: University of Nevada, Reno, Department of Electrical and Biomedical Engineering, Reno, NV, United States of America.|Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Ju
authors.initials: J
authors.lastname: Han
authors.affiliation: University of Nevada, Reno, Department of Electrical and Biomedical Engineering, Reno, NV, United States of America.|Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America.
authors.forename: Bahram
authors.initials: B
authors.lastname: Parvin
mesh_terms: D018929:Cell Culture Techniques; D019295:Computational Biology; D057166:High-Throughput Screening Assays; D006801:Humans; D061986:MCF-7 Cells; D008954:Models, Biological