TODO: helpful screenshots when the new GUI is ready.
With Shape-Out it is possible to convert deformation values to values of the Young’s modulus based on the numerical simulation work for fully elastic spheres by Mokbel et al. [MMM+17].
The “Calculate” tab allows you to obtain the Young’s modulus for the samples you selected for plotting.
Currently, the only model available is the elastic sphere. After choosing the type of measurement medium you must set the right temperature or – in case you choose “Other” – the correct viscosity. For CellCarrier media, the correct viscosity is automatically calculated according to the shear thinning behavior as analyzed in [Her17].
Once “Compute elastic modulus” is clicked, a plotting option for the Young’s modulus will become available.
A conversion can only be carried out for deformation and size values in a “valid region” that will be described in more detail below.
Events outside this region will disappear from the plot – also if the Young’s modulus is not selected for plotting. To plot the complete sample in those cases again, the checkbox “remove invalid events” in the “Filter” tab needs to be unchecked.
Valid Conversion Region¶
This section is meant to guide an experimental strategy to obtain results that can be converted to a Young’s modulus. Numerical simulations [MMM+17] have yielded a valid region for the conversion in the space of deformation and cell size shown with a color gradient for a 20 µm channel.
It is limited by regions A and B for objects too small and objects too large for reliable conversion. It is further limited for very small deformation values in region C. The reason for that is a very steep increase of E with little decrease in deformation that would yield potentially very large errors. Finally, it is limited by region D at larger deformation. In this region, simulations did not reach a stationary shape for the softer objects to be found there. Instead they became more and more elongated until they disintegrated by rupturing.
Therefore, as an experimental strategy, the goal of the experiment must be to choose the suitable channel size and to vary the flow rate such, that the results fall well within the valid region.
In order to make this process more comfortable, in the following, the valid regions are shown for the four standard channel sizes available. Those representations include an offset shift in deformation that would be expected in the experimental results due to the pixelation of the image as described in [Her17].
The values of the Young’s moduli in those regions will depend on the specific flow rate and the viscosity of the medium [MOG+15]. Note that in the illustrations that follow they merely represent a relative scaling and are not to be compared between illustrations.