Particle tracking

I am not sure what further protocol we can give you, as there is not really much futher information we could even provide.

As stated, 

1. we tracked the spots using Trackmate in Fiji (with the specified parameters). 

2. We used Morphometrics to get the cell outlines. 

3. as there is no good anbalysis tools in fiji to get real velocity (much less angle), we used custom matlab code, which is downloadable from the bitbucket account.  That gave all our poutputs, and all code used in our work is in that repo.

Basically, if you want to track particles. Fiji will do it. But that does not give any measures. If you want to analyze their veolcity or diffusion, you have to use cutsom code. There may be commerical programs that do this, but I am not aware of them (save imaris software, but that is really expenisve.)

So, I'm not sure if I can be of any more help here, in regards to the protocol. 

But if you can define your probelm a bit more   I might be able to help advise. (email me at egarner@g.harvard.edu)

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