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README.md

NeuTu - Software for Connectome Reconstruction

Publication to cite: NeuTu: Software for Collaborative, Large-Scale, Segmentation-Based Connectome Reconstruction, Ting Zhao*, Donald J. Olbris, Yang Yu and Stephen M. Plaza (2018)

Installation

NeuTu can be installed on a Mac or Linux machine. Its binary releases are available as conda packages. You can install it manually with conda commands or through the setup script.

Use Script (The Easiest Way)

curl -X GET https://raw.githubusercontent.com/janelia-flyem/NeuTu/develop/neurolabi/shell/setup_neutu.sh > setup_neutu.sh
bash setup_neutu.sh <install_dir> neutu-develop

Here <install_dir> is the installation directory.

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

<install_dir>/bin/neutu

Use Conda Commands

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-forge -c conda-forge neutu-develop

#For future update, you can run 'conda update -n <NAME> -c flyem-forge -c conda-forge neutu-develop' 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-forge -c conda-forge neutu-develop

#For future update, you can run 'conda update -n <NAME> neutu-develop -c flyem-forge -c conda-forge neutu-develop' 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 

Manual

Quick start

https://github.com/janelia-flyem/NeuTu/blob/master/neurolabi/doc/user_manual/neutu/quick_start.pdf

Full manual

https://github.com/janelia-flyem/NeuTu/blob/master/neurolabi/doc/user_manual/neutu/manual.pdf

For the most recent version

https://janelia-flyem.gitbook.io/neutu

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