README

Small demo on 3D volume stats with python.

Installation

$git clone https://github.com/bencardoen/nbr.git

Install MiniConda

In a shell:

$conda env create -f environment.yaml

If that fails (I've seen it fail on OSX), install deps manually (the env file has the complete list).

Running

$source activate nbr
$jupyter notebook

If your browser does not open, open it manually to url : 'localhost:8888'

Notebooks

• Imaris.ipynb Simple HDF5 exploration of .ims format

• Analysis Rory.ipynb Statistics on csv encoded segments