Software package for neuron reconstruction and visualization
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README.md

NeuTu

Software for proofreading EM connectomics

Installation

NeuTu can be installed on a Mac or Linux machine.

The Easiest Way

  1. Download setup_neutu_dev.sh

  2. Run 'bash setup_neutu_dev.sh <install_dir>', where <install_dir> is the installation directory.

Once the installation is done, you can launch the program by running

<install_dir>/bin/neutu

We use conda to manage our package, so you can also install the software in a more manual way with miniconda3.

Mac (OSX 10.12+ preferred)

curl -X GET https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > Miniconda-latest-MacOSX-x86_64.sh
bash Miniconda-latest-MacOSX-x86_64.sh

#Note: if the following command fails with some import error, you can unset PYTHONHOME and try again.
source <CONDA_ROOT>/bin/activate root
conda create -n <NAME> -c flyem neutu

#For future update, you can run 'conda update -n <NAME> -c flyem neutu' after activating miniconda.

Here <NAME> is the conda environment name. If you don't know what it is, just use neutu-env.

After successful installation, you should be able to lauch the application neutu.app in <CONDA_ROOT>/envs/<NAME>/bin.

Linux (Tested on Ubuntu 16.04, Fedora 16+ and Scientific Linux 7)

curl -X GET https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh

#Assuming miniconda is installed under <CONDA_ROOT>
#Note: if the following command fails with some import error, you can unset PYTHONHOME and try again.
source <CONDA_ROOT>/bin/activate root
conda create -n <NAME> -c flyem neutu

#For future update, you can run 'conda update -n <NAME> -c flyem neutu' after activating miniconda.

Here <NAME> is the conda environment name. If you don't know what it is, just use neutu-env.

After successful installation, you can launch the program with the following commands

source <CONDA_ROOT>/bin/activate <NAME>
neutu 

Windows

Not supported yet.

Manual

Quick Start: https://www.dropbox.com/s/cnewjf7bdm3qbdj/manual.pdf?dl=0

Full Manual: https://www.dropbox.com/s/w9sbry69v04tziu/NeuTu%20Manual%202018.pdf?dl=0