Info on modelPreprocessMovie

[Antorithms]

Hi, My name is Anto and I am relatively new to the use of Ciatah. First of all thank you, it's very very useful! I had a doubt concerning modelPreprocessMovie and in particular Registration_normalization and Movie_normalization as from the preprocessing options. Filtering and any parameters set in Registration_Noralization are only used to motion correct and not actually applied on the output movie, right? On the other hand, Movie_normalization parameters are used to filter the video and these filtering is actually kept in the output, correct?
Thanks a lot for the clarification! Best, Anto

[bahanonu]

Great to hear!

Regarding your question: yes, options under Registration_Noralization are used only for motion correction (as sometimes the corrections needed for improved registration are not the same as those needed for good cell extraction or visualization in later steps). Options under Movie_normalization are applied before motion correction is applied (but after registration coordinates obtained), as this avoids filtering issues with NaNs/zeros at the edge of the motion corrected frame.

See 3.14 Preprocessing of Ca2+ Imaging Data in our book chapter: https://link.springer.com/protocol/10.1007/978-1-0716-2039-7_13#Sec18.

Let me know if this helps or you need any further clarification.

[Antorithms]

That's great, thanks a lot for the explanation. Upon running MovieNormalization with matlab divide by lowpass with freqlow = 0 and freqHigh = 4 we got great results for cell extraction but some halos on the borders appeared as in the screenshot below. These halos are changing in intensity in time. Do you have any idea why they appear, if they are a problem and how to get rid of them ? thanks a lot again for the amazing software and help!