Usage Appendix: Parameter Selection

A lot of parameters are hard to get right. That’s why OrientationField is designed with trial and error computation in mind, where you can recompute the nematic field very quickly, to make sure it captures the information you are looking for. Of course, we recommed you stick to a set of parameters per experiment as to uphold FAIR principles.

In this section we’ll go through the computation parameters and provide a little explanation for each one.

Structure Width

You could guess the right structure width value based on your pixel size, if you know the size of your biological data very well. However, if the sizes of the objects in your image doesn’t vary much, you might not encounter a situation where changing this parameter does too much.

These such situations are where an image contains small structure whose orientation is different than that of the structure they form. Here is such an example:

Below is the resulting nematic field, after selecting a structure width of 2 on the left, or 64 on the right.