A recent paper published through a collaboration of our coordinator, UCL, with our Associate Partner at the Centre for Medical Informatics at the University of Edinburgh, outlines the use and release of the PolNet software tool. https://doi.org/10.1016/j.bpj.2018.03.032
PolNet is a software tool for the computer simulation of blood flow in realistic microvascular networks imaged with a wide variety of microscopy and clinical imaging techniques. To date, PolNet has contributed to: a) uncovering the relationship between blood flow and blood vessel biology and its importance for correct vascularisation of tissues, and b) developing ways of predicting retinal vascular damage in diabetic retinopathy patients. PolNet facilitates the adoption of cutting-edge computer simulation technology by non-experts in the Biosciences.
PolNet provides a complete workflow for image processing, three-dimensional vascular network reconstruction, and blood flow simulation with the HemeLB software. In addition, it provides tools for studying the relationship between the flow simulated and cellular/molecular readouts quantified in the same images. To date, PolNet has contributed to establishing the relationship between blood flow and endothelial cell polarisation and migration during vascular development. In addition, PolNet is being used to develop novel methods for the prediction of sight-threatening complications in diabetic retinopathy. PolNet uses the Docker platform to facilitate deployment in experimental biology laboratories and hospitals. PolNet allows execution of HemeLB simulations in both commodity software and High Performance Computing resources. Ongoing work is aimed at enabling HemeLB execution in Cloud resources.