Sailem, H. Z. | Search bioRxiv

bioRxiv2021

ShapoGraphy: a glyph-oriented visualisation approach for creating pictorial representations of bioimaging data

Intuitive visualisation of quantitative microscopy data is crucial for interpreting and discovering new patterns in complex bioimage data. Existing visualisation approaches, such as bar charts, scatter plots and heat maps, do not accommodate the complexity of visual information present in microscopy data. Here we develop ShapoGraphy, a first of its kind method accompanied by a user-friendly web-based application for creating interactive quantitative pictorial representations of phenotypic data and facilitating the understanding and analysis of image datasets (www.shapography.com). ShapoGraphy enables the user to create a structure of interest as a set of shapes. Each shape can encode different variables that are mapped to the shape dimensions, colours, symbols, and stroke features. We illustrate the utility of ShapoGraphy using various image data, including high dimensional multiplexed data. Our results show that ShapoGraphy allows a better understanding of cellular phenotypes and relationships between variables. In conclusion, ShopoGraphy supports scientific discovery and communication by providing a wide range of users with a rich vocabulary to create engaging and intuitive representations of diverse data types.

systems biology↗

bioRxiv2019

Multi-Parametric Profiling of Endothelial Cell Networks Reveals Functional Role of Glutamate Receptors in Angiogenesis

Angiogenesis plays a key role in several diseases including cancer, ischemic vascular disease, and Alzheimers disease. High throughput screening of endothelial tube formation provides a robust approach for identifying drugs that impact microvascular network formation and morphology. However, the analysis of resulting imaging datasets has been limited to a few phenotypic features such as the total tube length or the number of branching points. Here we developed a high content analysis framework for detailed quantification of various aspects of network morphology including network complexity, symmetry and topology. By applying our approach to a high content screen of 1,280 drugs, we found that many drugs that result in a similar phenotype share the same mechanism of action or common downstream signalling pathways. Our multiparametric analysis revealed a group of drugs, that target glutamate receptors, results in enhanced branching and network connectivity. Using an integrative meta-analysis approach, we validated the link between these receptors and angiogenesis. We further found that the expression of these genes correlates with the prognosis of Alzheimers patients. In conclusion, our work shows that detailed image analysis of complex endothelial phenotypes can reveal new insights into biological mechanisms modulating the morphogenesis of endothelial networks and identify potential therapeutics for angiogenesis-related diseases.

systems biology↗