how to select best alignment in msRUN?

[Chenglin]

In the msRun, it has one step ask me to select best alignment (Enter number), when it has a histogram there (attached image), but I am not clear how could I decide the best alignment based on that image. Could you help to give some advice? Thank you very much in advance!

[Daniel Aharoni]

Hi Chenglin,
You want to look for the following when selecting image alignment:

Top Plot: This is a histogram of the x and y shifts of each from across your recording. Generally if the motion correction algorithm worked well this 2d histogram should show all frames in a small cluster about 10px by 10px wide. If the motion correction performs poorly you often will she a much larger scattering in this 2d histogram.

Bottom Plot: This is just the mean frame of your data after applying the motion correction. Proper motion correction will result in a mean image with minimal blur.

You can also use msPlayAlignment() to see how well the motion correction did.