Miniscope Board
General Category => Data Analysis => Topic started by: Chenglin on May 16, 2017, 03:35:59 PM
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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!
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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.