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HomeHomeWelcome to Imar...Welcome to Imar...General LobbyGeneral LobbyTracking maggots from MPEG videos :-)Tracking maggots from MPEG videos :-)
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Tracking maggots from MPEG videos :-)
 

Hi everyone,

I'm working on a GUI XTension to track maggots (I think that's the scientific term) directly from movie files. So, from MPEG or AVI or whatever format FFMpeg can read. You can't just drop those files in Imaris, so you can either do the conversion to a TIFF stack in FIJI, or use an XTension to extract the frames and upload them to Imaris. The second method is a bit more streamlined as you can do some image processing as an intermediary step.

I thought (for the benefit of the student whose research this is) that I would demonstrate the different steps involved by linking a Jupyter Notebook to Imaris using my XTIPython XTension.

Here's what I came up with:

http://nbviewer.jupyter.org/github/zindy/Imaris/blob/master/tutorials/tracking_maggots.ipynb

The image processing isn't really exciting (background estimate, background subtraction, filtering, tracking) but the notebook demonstrates some cool tricks, like building a scene in Imaris, and adding / tracking surfaces programmatically using vImageProcessing.DetectSurfaces() and vImageProcessing.TrackSurfacesAutoregressiveMotion()

That's about it really. Hope someone else will find this useful.

I'll release the XTension on my github https://github.com/zindy/imaris when it's ready.

Cheers,
Egor

 
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