help > Cell morphology tracing over time
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Feb 8, 2017 10:02 AM | Lorena Arancibia
Cell morphology tracing over time
Hello
I would like to see how cell morphology changes over time. I have successfully traced my cells using Neuron APP2 and then used swc_to_mask to create a binary image of my cells in 3D which I then save as tiff and analyse using matlab. However, I would now like to do this for my entire data set (>200 cells with 60 different time points each) and so need to find a way to automate this. Ideally I would be prompted for the trace settings and the image size (for the mask) for each time series (which I currently have split into one image per time point- and all placed in a folder/ or can I load them as a 4D image and get Vaa3D to trace for each time point?).
I think I may have to do a new Plugin for this or perhaps I can code for it in Matlab and get it to communicate with Vaa3D (?), but I am not entirely sure how to go about it.
Any help will be most appreciated
Thank you
I would like to see how cell morphology changes over time. I have successfully traced my cells using Neuron APP2 and then used swc_to_mask to create a binary image of my cells in 3D which I then save as tiff and analyse using matlab. However, I would now like to do this for my entire data set (>200 cells with 60 different time points each) and so need to find a way to automate this. Ideally I would be prompted for the trace settings and the image size (for the mask) for each time series (which I currently have split into one image per time point- and all placed in a folder/ or can I load them as a 4D image and get Vaa3D to trace for each time point?).
I think I may have to do a new Plugin for this or perhaps I can code for it in Matlab and get it to communicate with Vaa3D (?), but I am not entirely sure how to go about it.
Any help will be most appreciated
Thank you
Feb 9, 2017 08:02 PM | Zhi Zhou
RE: Cell morphology tracing over time
For the first two steps: APP2 and swc_to_mask, you can use command
line for batch process. Please check this link (https://github.com/Vaa3D/Vaa3D_Wiki/wiki...).