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open-discussion > Tracking cell processes in 3D+t
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Jan 15, 2017 10:01 AM | James Drew - UCL
Tracking cell processes in 3D+t
Hi there,
I am building an analysis tool for tracking the movement of cell processes in 3D over time. My input data is a series of 3D single channel z-stacks of a single cell. My methodology for doing this is to:
(1) generate a 3D trace of the cell at each time frame using the Neuron2(APP2) plugin
(2) identify the tip markers in each SWC trace
(3) pair up the tip markers at each timepoint to generate tracking data (i.e. match end points in t0 and t1, t1 and t2... etc)
My question is about how best to do (3). I am thinking of using Vaa3D's 'trace a path between two landmarks' function to find a path through the cell (i.e. through a z-stack that is the sum of z-stacks t0 and t1) between each tip marker in t0 and t1 and pair the markers with the shortest trace distance. I want to ask 1) if this is a legitimate approach and 2) if there's anything like this already implemented with Vaa3D? It seems like 3D is perfectly suited for this sort of tracking so I'd be surprised if there isn't something already implemented, but I can't find it.
Hope that all makes sense.. Many thanks!
James
I am building an analysis tool for tracking the movement of cell processes in 3D over time. My input data is a series of 3D single channel z-stacks of a single cell. My methodology for doing this is to:
(1) generate a 3D trace of the cell at each time frame using the Neuron2(APP2) plugin
(2) identify the tip markers in each SWC trace
(3) pair up the tip markers at each timepoint to generate tracking data (i.e. match end points in t0 and t1, t1 and t2... etc)
My question is about how best to do (3). I am thinking of using Vaa3D's 'trace a path between two landmarks' function to find a path through the cell (i.e. through a z-stack that is the sum of z-stacks t0 and t1) between each tip marker in t0 and t1 and pair the markers with the shortest trace distance. I want to ask 1) if this is a legitimate approach and 2) if there's anything like this already implemented with Vaa3D? It seems like 3D is perfectly suited for this sort of tracking so I'd be surprised if there isn't something already implemented, but I can't find it.
Hope that all makes sense.. Many thanks!
James
Jan 17, 2017 10:01 PM | Hanchuan Peng
RE: Tracking cell processes in 3D+t
for help, please post in the Help
Forum...
Originally posted by James Drew:
Originally posted by James Drew:
Hi there,
I am building an analysis tool for tracking the movement of cell processes in 3D over time. My input data is a series of 3D single channel z-stacks of a single cell. My methodology for doing this is to:
(1) generate a 3D trace of the cell at each time frame using the Neuron2(APP2) plugin
(2) identify the tip markers in each SWC trace
(3) pair up the tip markers at each timepoint to generate tracking data (i.e. match end points in t0 and t1, t1 and t2... etc)
My question is about how best to do (3). I am thinking of using Vaa3D's 'trace a path between two landmarks' function to find a path through the cell (i.e. through a z-stack that is the sum of z-stacks t0 and t1) between each tip marker in t0 and t1 and pair the markers with the shortest trace distance. I want to ask 1) if this is a legitimate approach and 2) if there's anything like this already implemented with Vaa3D? It seems like 3D is perfectly suited for this sort of tracking so I'd be surprised if there isn't something already implemented, but I can't find it.
Hope that all makes sense.. Many thanks!
James
I am building an analysis tool for tracking the movement of cell processes in 3D over time. My input data is a series of 3D single channel z-stacks of a single cell. My methodology for doing this is to:
(1) generate a 3D trace of the cell at each time frame using the Neuron2(APP2) plugin
(2) identify the tip markers in each SWC trace
(3) pair up the tip markers at each timepoint to generate tracking data (i.e. match end points in t0 and t1, t1 and t2... etc)
My question is about how best to do (3). I am thinking of using Vaa3D's 'trace a path between two landmarks' function to find a path through the cell (i.e. through a z-stack that is the sum of z-stacks t0 and t1) between each tip marker in t0 and t1 and pair the markers with the shortest trace distance. I want to ask 1) if this is a legitimate approach and 2) if there's anything like this already implemented with Vaa3D? It seems like 3D is perfectly suited for this sort of tracking so I'd be surprised if there isn't something already implemented, but I can't find it.
Hope that all makes sense.. Many thanks!
James