Re: [bonsai-users] Analyzing fiber photometry output from Bonsai/Point Grey

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Gonçalo Lopes

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Jun 27, 2019, 10:00:12 PM6/27/19

to M.R., Bonsai Users

Welcome to the forums!

I believe you will find this question very useful. The second reply has the MATLAB version of the code:

https://groups.google.com/d/topic/bonsai-users/WD6mV94KAQs/discussion

Hope this helps.

On Thu, 27 Jun 2019 at 22:51, M.R. <Samantha...@gmail.com> wrote:

Hi!
I'm brand new to MATLAB/Bonsai/Fiber photometry.

I've gotten some help from this forum, like changing the point grey times to actual usable time stamps.

I've attached the csv file im working with.
column 1= point grey time stamps
c2= 410 channel in VTA
c3= 470 channel in VTA
c4=410 channel in mPFC
c5= 470 channel in mPFC

the 470 channels are the isosbestic and the 410 is the fluorescent output of interest for each region.

So if im trying to remove artificact would I just be subtracting the 410 data from 470?

After that I'm not really sure what to do with the data....

does anyone have any MATLAB scripts to help?

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M.R.

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Jun 28, 2019, 2:26:40 PM6/28/19

to Bonsai Users

Sorry! Accidentally deleted my original post....

Hi!

I'm brand new to MATLAB/Bonsai/Fiber photometry.

I've gotten some help from this forum, like changing the point grey times to actual usable time stamps.

I've attached the csv file im working with.

column 1= point grey time stamps

c2= 410 channel in VTA

c3= 470 channel in VTA

c4=410 channel in mPFC

c5= 470 channel in mPFC

the 470 channels are the isosbestic and the 410 is the fluorescent output of interest for each region.

So if im trying to remove artificact would I just be subtracting the 410 data from 470?

After that I'm not really sure what to do with the data....

does anyone have any MATLAB scripts to help?

On Thursday, June 27, 2019 at 7:00:12 PM UTC-7, goncaloclopes wrote:

Welcome to the forums!

I believe you will find this question very useful. The second reply has the MATLAB version of the code:
https://groups.google.com/d/topic/bonsai-users/WD6mV94KAQs/discussion

Hope this helps.

On Thu, 27 Jun 2019 at 22:51, M.R. <Samanth...@gmail.com> wrote:

Hi!
I'm brand new to MATLAB/Bonsai/Fiber photometry.

I've gotten some help from this forum, like changing the point grey times to actual usable time stamps.

I've attached the csv file im working with.
column 1= point grey time stamps
c2= 410 channel in VTA
c3= 470 channel in VTA
c4=410 channel in mPFC
c5= 470 channel in mPFC

the 470 channels are the isosbestic and the 410 is the fluorescent output of interest for each region.

So if im trying to remove artificact would I just be subtracting the 410 data from 470?

After that I'm not really sure what to do with the data....

does anyone have any MATLAB scripts to help?

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M.R.

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Jun 28, 2019, 2:28:10 PM6/28/19

to Bonsai Users

Thanks, I have seen that post and used it to decode the timestamps. Now I'm trying to figure how to remove artifact if anyone knows... :)

On Thursday, June 27, 2019 at 7:00:12 PM UTC-7, goncaloclopes wrote:

Welcome to the forums!

I believe you will find this question very useful. The second reply has the MATLAB version of the code:
https://groups.google.com/d/topic/bonsai-users/WD6mV94KAQs/discussion

Hope this helps.

On Thu, 27 Jun 2019 at 22:51, M.R. <Samanth...@gmail.com> wrote:

Hi!
I'm brand new to MATLAB/Bonsai/Fiber photometry.

I've gotten some help from this forum, like changing the point grey times to actual usable time stamps.

I've attached the csv file im working with.
column 1= point grey time stamps
c2= 410 channel in VTA
c3= 470 channel in VTA
c4=410 channel in mPFC
c5= 470 channel in mPFC

the 470 channels are the isosbestic and the 410 is the fluorescent output of interest for each region.

So if im trying to remove artificact would I just be subtracting the 410 data from 470?

After that I'm not really sure what to do with the data....

does anyone have any MATLAB scripts to help?

--
You received this message because you are subscribed to the Google Groups "Bonsai Users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to bonsai...@googlegroups.com.

Gonçalo Lopes

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Aug 9, 2019, 5:25:57 AM8/9/19

to M.R., Bonsai Users

Hi Samantha,

Sage Aronson from Neurophotometrics has been kind enough to share an example MATLAB script he wrote to normalize calcium dependent data using the isosbestic control signal. The script works with the example play data (also attached) recorded by Tom Kash's lab at UNC Chapel Hill, collected by his graduate student Olivia Hon.

Hopefully this will help you work with your recorded data format as well.

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