ROI sellection for Miniscope Capture?

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Kenneth Dyson

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Dec 10, 2020, 3:01:23 PM12/10/20
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Hi Daniel,
I am wondering if there is a way in the config file to select an ROI for the miniscope recording, similar to what is available in the behaviour recording?
Using the latest Miniscope-QT software and DAQ firmware with v4 and v3 scope.
Thanks,
Ken

Daniel Aharoni

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Dec 10, 2020, 5:08:20 PM12/10/20
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Hi Ken,
This is a good suggestion. I'll try to add this to the next release of the software.

Kenneth Dyson

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Dec 10, 2020, 6:55:39 PM12/10/20
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Thanks Daniel!!!!

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Daniel Aharoni

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Dec 11, 2020, 11:08:46 PM12/11/20
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Hi Ken,
you had good timing for your suggestion as I just started working on the next release of our software a day ago. I have now added in ROI control to the code in our "dev" branch of the Software repo and it will be included in the next release. Will aim to have everything done and released by the end of the year.

Martin Jendryka

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May 18, 2022, 7:11:19 AMMay 18
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Hi,
 I realized that the avi files, where the ROI selection window was used during the recording, cannot be read correctly using the MATLAB 'read' function. You get a distorted image similar to the one you see below.  I suppose that neither ImageJ nor MATLAB can handle the non-standard aspect ratio (in this example it is 398x332).  I used ffmpeg to pad black frames on the borders to get an even aspect ratio (400x400). Then MATLAB was able to handel it. However, these files are compressed (from grey to fmp4), so I am not sure what I am losing here. Traces look fine after extraction using PCAICA.    
Still, I would be very careful using the ROI selection tool since it can prevent loading the videos correctly in MATLAB.

Best,
Martin 
Capture.PNG

Daniel Aharoni

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Jun 17, 2022, 12:06:05 AMJun 17
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Hi Martin,
I haven't seen this issue before and I think cropped Miniscope and behavior videos have loaded up fine for me in imageJ. Would it be possible for you to share a .AVI file that has this issue?

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