NBCR Summer Training Program - "Data to Structural Models"

This week-long intensive program introduces students to principles, methods, and NBCR tools for generating high-quality three-dimensional meshes for numerical analysis in multi-scale modeling of subcellular, cell, tissue, and organ biophysics. Structural models will be derived from structural data obtained primarily from 3D imaging modalities, including electron tomography, multi-photon and confocal microscopy, and whole-body medical imaging modalities like CT and MRI.

  1. GAMer
  2. Kepler Workflow System

Day 1: Introduction to NBCR image analysis and segmentation tools. Segmenting large electron microscopic image volumes.

The following tools are required for Day 1:
Tool 1. A web browser (e.g. Firefox, Chrome)

Tool 2. The IMOD software package, a set of image processing and visualization tools for microscopic data:
For Windows:
Download the appropriate ‘clickable installer’ from:
Run the downloaded ‘.exe’ file and choose to install IMOD with the default options.
Note: The clickable installer will also install Cygwin, a UNIX-like terminal program necessary for IMOD. The default install path for Cygwin should be along the lines of C:cygwin64. The default install path for IMOD would then be C:cygwin64usrlocalIMOD
Verify that you can open the IMOD GUI, 3dmod. Open Cygwin and, at the command line, type ‘3dmod’ (without the quotes) and hit enter.

For Mac:
Download the appropriate installer from:
Follow the installation instructions at:
Verify that you can open the IMOD GUI, 3dmod. At the Terminal, type ‘3dmod’ (without the quotes) and hit enter.

For Linux:
Download the appropriate installer from:
Follow the installation instructions at:
Verify that you can open the IMOD GUI, 3dmod. At the command line, type ‘3dmod’ (without the quotes) and hit enter.

Tool 3. An SSH client:
For Windows:
The Cygwin client that was installed with IMOD is sufficient.

For Mac/Linux:
The default Terminal programs are sufficient.

Day 2: Modeling and Computing using Kepler Workflows.

Virtual Box Installation Instructions

Preparation: These instructions describe how to install VirtualBox that will be used in this class’s Hands-On sessions.
Download and Install VirtualBox (if you don’t already have it installed.)

Step 1: Go to
Step 2: Download the VirtualBox platform package for your operating system.
Step 3: Once the download completes, install VirtualBox and start it.

Day 3: Blender and HexBlender

Lecture Material
Download version 2.75a from Blender software for your operating system.
For both systems you can simply download a zip file, extract it and then run it.
Mac: It’s best to run Blender from the Terminal (/Applications/Utilities) to view any diagnostic information. Something like the following works:
Windows users can access a terminal window within Blender at Window -> Toggle System Console, so there is no need to run it from a command window

Anaconda – Python version 3
Our Blender addon needs some additional Python packages and Anaconda provides those for us.
Anaconda Python Suite
It should auto-detect your operating system, just be sure to install the Python 3 version.
Mac and Windows: The easiest thing to do is to simply create a PYTHONPATH variable that points to Anaconda’s site-packages directory.
Mac: For a per-time use, just enter the following in the Terminal window before starting Blender:
export PYTHONPATH=$HOME/anaconda/lib/python3.4/site-packages
You’ll need to do this every time you open a new Terminal window, or you can create an alias and put that into your startup file, ex:
alias blender275='/Applications/Blender275a/' Windows: You will likely need to add a new system variable with the similar information:
Windows 7: Start -> Right Click Computer -> Properties -> Advanced -> Env Settings
Windows 8: Search for system environmental variables

Download most recent version at:
HexBlender Addon
You do not need to unzip the file and you can install it by first starting Blender.
Then go to File -> User Preferences -> Add-ons -> Install from File and select the zip file.
Type ‘hex’ into the search window and that should show our addon.
You’ll need to check the box in the upper right-hand corner of the addon to actually activate it. You will see error messages if it doesn’t work.
Lastly, be sure to select the ‘Save User Settings’ button at the bottom so that the HexBlender addon will always be enabled when starting Blender.

Blender model file: BlenderDemo-Final.blend
Blender Reference file: Blender Reference Guide

Day 4: Continuity

Download the most recent version (8228) from:
Continuity Downloads
Mac and Windows have auto-installers and should go smoothly. Please let me know if that is not the case.
Linux, after downloading you simply need to extract the file, something like:
tar zxvf cont6_4_1_8228_linux64.tgz
cd continuity
Windows: It is preferable to not install Continuity in the Program Files directory.
Continuity requires write permission to the directory where it is installed and to not have to continually get approval notices,
we recommend installing it elsewhere.
Mac: If you do not have either a C compiler or the autoconf command on your machine, you will need to install the following:
Mac Build Tools

Files for EP rendering example: EP Rendering Example
Files for Fitting example: Fitting Files

Day 5: