How can I choose the mode: conservative, liberal, linear to decide whether they are some neurons across days? I am not sure if I understand how to do it properly.

[Virginia9733]

Thank you for developing this wonderful tool.

May I ask a question: How can I choose the mode: conservative, liberal, or linear to decide whether there are the same neurons across days? I am not sure if I understand how to do it properly.

As indicated in Figure 5 in the paper.
https://www.nature.com/articles/s41592-024-02440-1/figures/5

[EnnyvanBeest]

In our experience, the default (intermediate) method works best. It acts conservatively for subsequent days but liberally for days that are far apart.
You can always compare for which of the methods the functional metrics (e.g. ISI AUC values) are better. For figure 5 we used the following code to do this: https://github.com/EnnyvanBeest/UnitMatch/blob/main/MATLAB/Paper_Figures/summaryMatchingPlots.m