df/f traces plotting and generate video files (raw data, df/f)

[Najetserradj]

First of all, I want to say thank you greatly to all miniscope members for thier interest to this project.

I am running msRun.m function and I have few questions as I am very naive in Matlab:
 
1) In which step of the analysis script should I type a function (please provide details) in msRun.m to plot df/f traces for individual firing cell through the time?
2) I was not able to find or download the script that is used to generate a video file of the processes traces that shown in main page (raw data and df/f). Please can you advice when should I use this in msRun.m as well?
3) How can we select manually only some segments from the video to plot df/f?
4) How do we extract firing when using msRastorPlot.m
5) Extract df/f traces seems showing the y axis as frames numbers, but what is the x-axis and it unit?
6) How to distinguish between individual cells firing through the frames ?
Best,
najet.

[Daniel Aharoni]

Hi Najet,
1) In which step of the analysis script should I type a function (please provide details) in msRun.m to plot df/f traces for individual firing cell through the time?
After you extract and clean traces (msExtractdFF) you can run msRasterPlot to plote individual firing of cells. The firing of detected cells is stored in ms.firing and ms.trace.
2) I was not able to find or download the script that is used to generate a video file of the processes traces that shown in main page (raw data and df/f). Please can you advice when should I use this in msRun.m as well?
You can run this once you run alignment and extract the background of the video.
3) How can we select manually only some segments from the video to plot df/f?
I do not have a script that allows you to manually select segments. This should be pretty easy to implement.
4) How do we extract firing when using msRastorPlot.m
msRasterPlot just displays dF/F traces and deconvolved firing once you have run the appropriate portion of msRun.
5) Extract df/f traces seems showing the y axis as frames numbers, but what is the x-axis and it unit?
I am a bit confused here. It depends on how you are displaying the df/f traces. You can look into the specific function to see how it is being plotted.
6) How to distinguish between individual cells firing through the frames ?
Can you clarify what you mean here?

[Jesper.vernooij]

About msRasterPlot: deconvoluted calcium bursts are depicted with a red line with or without a black lined centre.
    Q: What doe the Red and Black line represent? (what is the difference between a red line with and without a black lined centre?)

Thank you!

[Najetserradj]

Regarding point 6). How can we match each segment across a session? I would like to get the map showing the identified segment and for each colored identified segment match the colored df/f trace.
best,

[Najetserradj]

I have two questions:

1) I used msGenerateVideoObj.m to get the raw video along side with the motion corrected df/f as shown in main page but not sure why did not work for me. please advice.
2) I have a video of 10 min recording, there is any possibility to analyze just the first 5 min, if so, how should I do it?

[Daniel Aharoni]

Hi Najet,
Unfortunately I do not have time to answer specific questions on analysis. You can open up each MATLAB function and walk through what the code is actually doing.