Forum - Data analysis basic questions.

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Hi all, I have some basic data analysis questions:

- What do you take into account when selecting the fluorescence value threshold for spike activity, and what would make a good threshold? (somewhere between mean and max?)

- In the ROI selection of msBatchSelectROI, should you select single neurons as ROIs (multiple ROS's) or do you select the general area you want to align (1 to 3 ROIs)?

I know the answers to these questions can vary based on what one tries to analyze, in my case I'm looking to increase the (neuron)signal to (background)noise ratio when trying to isolate single neuron dF/F.


Posted by Jesper.vernooij on 14 March 2016 at 18:22.
Edited by Jesper.vernooij on 14 March 2016 at 18:22.

Hi Jesper, the flourescence value threshold should is a way for us to eliminate frames where things have gone wrong with either the LED or the camera sensor. We have tried hard to make it so that things don't go wrong, but if there are frames where the LED flickers off (for instance), then this is a way to eliminate those frames. If you do not have any issues with your recording you should generally just pick a value below the mean so that nothing gets eliminated.

msBatchSelectROI is used to set ROIs for alignment. Here you want to select a fairly large region with any blood vessels that are in your image. You want to avoid anything that does not track with the alignment of the image (like small specs of dirt on the camera). I recommend playing with it and you will see how changing the ROI can change the alignment.

To play with the SNR you may consider changing what the program is considering as F. I believe our current program uses the mode of the signal, but this can be played with as well (in msExtractdFFTraces).

Posted by Tristanshuman (administrator) on 14 March 2016 at 23:24.

Thank you!

Posted by Jesper.vernooij on 15 March 2016 at 16:13.