Author Topic: how to select best alignment in msRUN?  (Read 2540 times)

Chenglin

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how to select best alignment in msRUN?
« on: May 16, 2017, 03:35:59 PM »
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

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Re: how to select best alignment in msRUN?
« Reply #1 on: May 20, 2017, 12:52:37 PM »
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.