Herzog, WalterFederico, SalvatoreSibole, Scott C.2016-05-042016-05-0420162016Sibole, S. C. (2016). pyCellAnalyst: Extensive Software for Three-dimensional Analysis of Deforming Cells (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/27488http://hdl.handle.net/11023/2966Laser scanning microscopy has proven to be a transformative tool in the biomedical sciences. The technology provides a means to image three-dimensional, time-varying, micro-scale features within living tissue, which in turn has borne exciting avenues for the experimental investigation of the relationship between the hierarchical spatial scales within organisms. By coupling laser scanning microscopes to mechanical testing systems, one can study the relationships between mechanics at the organ, tissue, and cellular scales. In practice, while a controlled mechanical state is applied to intact tissue, images of the cells within can be obtained via microscopy; however, extracting the geometric information from these images and characterizing deformation has been a challenge to the field. pyCellAnalyst is an extensive software framework for such analysis of these image data. It provides an accessible interface to reconstruct cellular geometries from images, characterize deformation, and perform finite element analyses informed by the experimental observations.engUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.Computer ScienceEngineering--BiomedicalEngineering--MechanicalMicroscopyChondrocyteImage ProcessingMultiscaleFinite ElementImage SegmentationContinuum MechanicsArticular cartilagemaster thesis10.11575/PRISM/27488