Question about polarity measures

[Siobhan Braybrook]

Hello! We were wondering about the difference between using Wall Min and Cell Average for polarity display/calculation.....

Are there case where you might use one over the other? It seems Naomi used Wall Min (?)

Thanks!

[Pierre Barbier de Reuille]

Hello, so what happens if the following: when computing the polarity, you want to normalize the intensity of the cell wall independently for each cell. And for this you have two choices:

1. You normalize w.r.t. the minimal signal on any wall within the cell.
2. You normalize w.r.t. the average intensity within the cell.

You should see the difference as in case 1 the resulting signal is always greater or equal to 1, while in the second case, it will be 1 on average. In the end, I think the case 1 is simpler to interpret: the value is the relative amount of signal on that wall compared to the weakest wall in the cell. Of course, another normalization could have been w.r.t. the maximal intensity of any wall within the cell.

Note: Be careful with using the polarity option of the heat map! The results are extremely dependent on the quality of the segmentation and the precise position of the boundary between cells. You need a way to check the correctness of your polarity.

[Pierre Barbier de Reuille]

In absence of feedback, I assume the answer was satisfying.