8000 SNR data export · Issue #71 · bahanonu/ciatah · GitHub
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SNR data export #71

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laopenti opened this issue Apr 20, 2021 · 2 comments
Open

SNR data export #71

laopenti opened this issue Apr 20, 2021 · 2 comments

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@laopenti
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Hi, Biafra~

Lately, I've been working on a two-photon .tiff file through computeManualSortSignals on MatLab 2020b, win10. Normally, all things pretty good so far. Thank you for the update version2.5.1, it's amazing.

Could you please concretely enlighten a handy approach or code to help me to export the SNR value of every identified cell while or finishing the computeManualSortSignals part. I could only read it from the interface like below on-by-one.

Biafra_参数含义02

If there is no misunderstanding on SNR here in CIAtah v2.5.1, that is Signals Noise Ratio, an important parameter I would use someday. So, hope you would help me with that.

And, one more thing, have you ever considered uploading a teaching video on the Internet about the rest of the operation after computeManualSortSignals?

Best Wishes to you!

Benson
from SheepMountain, NJ
@bahanonu
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hey Benson, great to hear things are working out for you. To grab the SNR you can load in the already processed data then compute SNR as below:

% Load data
[inputImages,inputSignals,infoStruct,algorithmStr] = ciapkg.io.loadSignalExtraction('path_to_file.mat');

% Compute SNR
inputSnr = computeSignalSnr(inputSignals,'detectMethod','raw','numStdsForThresh',2);

re: after computeManualSortSignals, are there specific steps or analyses you are referring to? We'll have a book chapter out soon that covers some later steps, e.g. comparing neural activity to behavior/stimuli.

@laopenti
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Hi, Biafra

Thanks fo 5F22 r the reply so quickly.

  • The grabbing is smoothly with your code demonstrated above, which is significant for my job-to-do.

  • Frankly speaking, I am a novice on CalciumImagingAnalysis and NeuralScience. There are so many analysis jobs I should- and would- do. Such as time-frequency analysis within a single neuron or a given population, classified neuron spatial correlation analysis. Each of them seems worthy yet intricacy to handling. I have to learn some other knowledge and Matlab skills to accomplish the later steps.

  • So, it is terrific to acknowledge that the new book chapter comes out soon which covers some later steps.

  • We will follow your great algorithm persistently and looking forward to other more powerful processing approaches.

Benson
From SheepMountain, NJ

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