Extracting Motion Corrected recordings from Suite2p

[freyapanchamia]

I was wondering how to export the motion corrected video from suite2p. After clicking on registered binaries, I would like to export the video available there. I tried reg_tif= True but that didn't give me the desired output. Any suggestions would be appreciated

[generalciao]

If you want the motion corrected movie in TIFF format, you should set the corresponding option to true before you run the suite2p pipeline. It sounds like you did not do that. Try setting reg_tif=True as you described, leave all output files where they are from the initial run, then re-run the suite2p pipeline. If all goes well, suite2p will know that it does not need to do everything (motion correction, extraction, etc) again, and will simply convert the binaries to TIFF. FYI, I have not tried that myself.

[freyapanchamia]

I did set reg_tif to true prior to running the suite2p pipeline. This created a reg_tif folder with various tiff files in it. I was wondering if I could extract the movie itself instead of just the tiff files

[generalciao]

You can import the TIFF sequence to ImageJ as a stack, then export from ImageJ as a .avi movie file. In doing so, you can select a compression level that is appropriate for your needs. Alternatively, if you are comfortable with python scripting, there are libraries available to do the conversion without using ImageJ.

If your movie has many frames, depending on your computer, this can be a slow process.

If suite2p has a feature to convert the binary movie directly to a compressed movie file (.avi for example), I have not seen it myself. Perhaps someone else can jump in.