Data analysis on videos gathered with different software

[Nadine]

Hello,

we have made our first Ca2+ imaging experiences with a different scope (but are now in the process of moving to the miniscope). The software provided by the company (Mosaic) is limited and I was wondering if anybody has tried to process these images with codes shared here. I am very new to Matlab and am I not sure if the provided scripts could be modified in order to be useful for this purpose. I can convert the movies to .avi files. But if I understand correctly the matlab scripts require the movie to be split into chunks of 1000 frames plus the data file with timestamps, is that right? Are the timestamps only necessary for synchronising the Ca2+ video with the behaviour or also if there is no behavioural video to be synced.

Any help to put me onto the right track (if there is any at all) would be very much appreciated.

Best
Nadine

[Daniel Aharoni]

Hi Nadine,
The videos do not need to be in chunks of 1000 so a single large uncompressed .avi file should work. The timestamp file is only needed for syncing the Ca2+ data to behavior. When extracting dF/F traces the script will require timestamps but you can generate these by running something like ms.time = linspace(0,ms.numFrames*1000/30,ms.numFrames); where 30 is the framerate the scope was running at.

We are in the process of switching over to a new analysis pipeline using CNMF. I would suggest you look into that as well.

[Nadine]

Hi Daniel,

thank you so much for your reply. I'll try to follow your recommendations!

Nadine