Innovation and Partnerships Office

BioSig3D: Software for Integrated Imaging and Profiling of 3D Cell Culture Models 2013-177, 2014-024


  • Analysis of 3D cell culture model systems
  • Oncology research and drug development
  • Couples novel image analysis algorithms with 3D microscopy


  • End-to-end solution — from assay to bioinformatics
  • Enables 3D visualization and analysis of 3D spatial data
  • Quantifies subcellular morphometric indices and corresponding molecular endpoints, on a cell-by-cell basis
  • Provides quantitative measures for the analysis of aberrant multicellular organization


BioSig3D is a computational platform for high-content screening of three-dimensional cell culture models that are imaged in 3D. BioSig3D provides an end-to-end solution for designing screening assays, provides novel algorithms for quantitative analysis, enables visualization of 3D spatial data, and integrates advanced bioinformatics analysis. BioSig3D can reduce the cost of evaluating therapeutic compounds and serve as a bridge between 2D cell culture models and animal testing.

BioSig 3D has six primary components: Resource Manager, Experimental Design Manager, Data Load Manager, Visualization modules, Image analysis methods, Bioinformatics modules.  Evaluation and testing have been conducted with cell lines with significant genetic diversity and distinct phenotypical signatures. Comparison of the Berkeley Lab technology with alternative methods demonstrates superior performance, in terms of error rates. Furthermore, BioSig 3D has identified indices that capture aberrant and normal morphogenesis in these four cell lines.

A brief introduction and demonstration of the BioSig3D is posted on YouTube. Click here or the link below for the reserachers’ publication on this technology.

STATUS: Software available for licensing. Go here for details.


Bilgin, C. C., Kim, S., Leung, E., Chang, H., Parvin, B. “Integrated profiling of three dimentional cell culture models and 3D micropscopy,” Bioinformatics, Vol. 29, No. 23 2013, pp. 3087-3093.