How do you trace neurons?

[matsut...@gmail.com]

Hi, I just found your nat package in R and I was browsing through different functions. 

It was however unclear to me how you get the skeletonized, or traced objects from the raw images. 

Are you using amira or ImageJ (Simple Neurite Tracer) for neurite tracing and then importing it to nat, or can you create these in nat as well?

[Greg Jefferis]

Dear matsutakehoyo,

Thank you for your interest in nat. This package has many functions for analysing neuronal morphology, but does not really provide any support for tracing images directly.

We have used both Amira and ImageJ (Simple Neurite Tracer) in the past and nat can read both the native output format of these programs as well as the standard SWC format. Other options for tracing include neutube and vaa3d.

The only exception to this is if you want to prepare neurons in the “dotprops” or vector cloud format used by the NBLAST algorithm. If you skeletonise a binary version of your neuron images in Fiji/ImageJ and save to nrrd format, you can then convert the nrrd image stack to a 3D vector cloud format using the dotprops function

http://jefferis.github.io/nat/reference/dotprops.html

Best wishes,

Greg Jefferis.

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[matsut...@gmail.com]

Hi Greg 

Thanks for your prompt reply! 

We have tried ImageJ for tracing, and I was hoping your tools offered something more for tracing. We would like to develop a routine to analyze large amounts of data, so we are looking for a way to trace dendrites automatically. Your tools look very interesting once we have traced the neurons, I hope I can find a way to quickly trace neurons and apply your tools! 

Regards

[Greg Jefferis]

Dear matsutakehoyo,

 

We have tried ImageJ for tracing, and I was hoping your tools offered something more for tracing. We would like to develop a routine to analyze large amounts of data, so we are looking for a way to trace dendrites automatically. Your tools look very interesting once we have traced the neurons, I hope I can find a way to quickly trace neurons and apply your tools!

I would recommend that you take a look at neutube (https://www.neutracing.com). If you have good quality images you can get quite nice results with a high degree of automation with this program.

All the best,

Greg.