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neurodata / brainlit

Method container for computational neuroscience on brains.
http://brainlit.neurodata.io/
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Apply DeepNeuron alg to mouselight data #121

Open tathey1 opened 4 years ago

tathey1 commented 4 years ago

DeepNeuron is a deep learning based algorithm for neuron reconstruction. Paper is here.

Does it work well on our data?

tathey1 commented 4 years ago

I believe Alisha tried this out briefly but ran into an obstacle - what was it again? @alishakodibagkar

alishakodibagkar commented 4 years ago

I had some issues running it on a Mac specifically. The paper offers 2 different options to run DeepNeuron: 1) The DeepNeuron plugin is included here as a plugin in releases of Vaa3D but this seems to only be provided for Linux operating systems (preferably CentOS). I tried to build a CentOS virtual machine but I'm not sure if that's the best way to go. 2) The DeepNeuron source code is provided here and you will have to build it as a C++ plugin of Vaa3D. This will likely work for MacOS/Linux/Windows, but I didn't get it to work, since I was only working on this for a week or so.

Vaa3D is a large image visualization and analysis software, and can be downloaded here

bvarjavand commented 4 years ago

@alishakodibagkar I think it's worth building the Vaa3D plugin, I imagine that platform has other algorithms to be tested as well? As you go along, please add a markdown file documenting the steps you took to get it working.

ryanlu41 commented 3 years ago

Was anyone able to find a way to build the plugin for Windows?

shreyasingh1 commented 3 years ago

@ryanlu41 I'm currently working on getting the existing plugin running on a CentOS machine as a proof of concept, but I should start working on building a Windows plugin with the source code in the upcoming week or so.