Within the Fortissimo 2 project SURFsara works with Electric Ant Lab on the realization of a virtual lab for microfluidic devices. Designing and engineering a microfluidic and lab-on-a-chip devices is a challenging task, particularly in health applications involving the flow and analysis of blood. The device design typically involves many trial-and-error iterations, which is both expensive and time-consuming. HemoSphere will offer a fully virtual counterpart to physical testing. The simulation combines sophisticated numerical techniques and modern parallelization using GPUs to calculate accurate, validated cell-mechanics, blood flow and biochemical dynamics.
An important part of the virtual lab is performing interactive data analysis of simulation results. The basis for this analysis is the Jupyter Notebook system, which provides an easy-to-use and flexible interactive Python environment. Within the HemoSphere project SURFsara focuses on developing interactive rendering of 3D cell data and volumetric data within the Jupyter Notebook.
An important element to this flexible and interactivity within these jupyter-notebooks are the IPywidgets. By making custom IPywidgets you can view and interact with you visualizations and save the current state of the visualization by just simply saving the Jupyter-notebook itself.
The implementation of the visualizations is partly based on ipyvolume, to which we are contributing most of the code developed within HemoSphere.