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Schroeder-Lab / Data

For pre-processing raw data (two-photon, ephys, bonsai, ...) and loading/saving data.
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Register_zstack function improvements #26

Closed mariacozan closed 1 year ago

mariacozan commented 1 year ago
  1. There is a note in the function description (piezo) which might need to be acted upon:

Note: need to add more input arguments depending on how registration works. Piezo movement might need to provided in units of z-stack slices if tiff header does not contain information about depth in microns

  1. A variable is never used (proportionTravelled) and should be removed (together with other variables that lead to it) unless it needs to be implemented (however it does not appear to be needed). 
    depthDiff = np.diff(piezo)
totalDepthTravelled = sum(depthDiff)
proportionTavelled = depthDiff / totalDepthTravelled

3.There are a few lines of commented out code which should be removed (see in function).

liadJB commented 1 year ago

2,3 - done. with 1 I am not sure I fully understand. the piezo data is always in microns. And this is what we want to use.

sylviaschroeder commented 1 year ago

Just saw this message. I don't see any context so I'm not sure what exactly this is about. I just wanted to note that bonsai probably record voltage from the Piezo, not microns. Sorry if I'm saying something you already know!

Sylvia

From: liadJB @.> Sent: Friday, September 15, 2023 11:00:35 am To: Schroeder-Lab/Data @.> Cc: Subscribed @.***> Subject: Re: [Schroeder-Lab/Data] Register_zstack function improvements (Issue #26)

2,3 - done. with 1 I am not sure I fully understand. the piezo data is always in microns. And this is what we want to use.

— Reply to this email directly, view it on GitHubhttps://github.com/Schroeder-Lab/Data/issues/26#issuecomment-1721008806, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADCZ37QCXXER3KCQYG3RUIDX2QRMDANCNFSM6AAAAAAU6JA6TA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

liadJB commented 1 year ago

I assume so given it recieves voltage signal from the NI. The function converts it to microns.

On Sat, 16 Sept 2023, 11:12 Sylvia Schröder, @.***> wrote:

Just saw this message. I don't see any context so I'm not sure what exactly this is about. I just wanted to note that bonsai probably record voltage from the Piezo, not microns. Sorry if I'm saying something you already know!

Sylvia

From: liadJB @.> Sent: Friday, September 15, 2023 11:00:35 am To: Schroeder-Lab/Data @.> Cc: Subscribed @.***> Subject: Re: [Schroeder-Lab/Data] Register_zstack function improvements (Issue #26)

2,3 - done. with 1 I am not sure I fully understand. the piezo data is always in microns. And this is what we want to use.

— Reply to this email directly, view it on GitHub< https://github.com/Schroeder-Lab/Data/issues/26#issuecomment-1721008806>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ADCZ37QCXXER3KCQYG3RUIDX2QRMDANCNFSM6AAAAAAU6JA6TA>.

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