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Beamline 8.3.2: MicroCT at the ALS

About BL 8.3.2

Welcome to the Python bitbucket page for beamline 8.3.2 at the Advanced Light Source. Beamline 8.3.2 is a synchrotron-based hard X-ray Micro-Tomography instrument. It allows non-destructive 3-dimensional imaging of solid objects at a resolution of approximately 1 micron. See our website here.

This repo contains Python tools for processing BL 8.3.2. For a repo containing ImageJ tools, see this repo.

Installing Xi-cam

We highly recommend using either Linux or Mac if you would like to install Xi-cam, as tomopy is not supported on Windows.

Linux

This installation requires conda for Python 2.7. If you do not have conda, please download it first here.

Download the xi-cam_env.yml file from this repo. In a terminal, go to the directory where the yml file was downloaded. For example, if it was downloaded to '/home/alsmicroct/Downloads/xi-cam_env.yml', type

cd /home/alsmicroct/Downloads/

Then run the following commands:

conda env create -f xi-cam_env.yml
source activate xi-cam

This will activate the conda environment. Typing xicam into the terminal with the activated environment should run Xi-cam. To deactivate the environment, enter source deactivate in the terminal.

One problem you may run into is that the PySide version prescribed in the xi-cam_env.yml file may not work for your operating system. The following systems should use the corresponding PySide version:

  • PySide 1.2.0: CentOS 7; Ubuntu 14, 16
  • Pyside 1.2.1: openSUSE

The default PySide version is 1.2.0. To install 1.2.1, run the following command with the conda environment active:

conda install pyside=1.2.1

You can also install 1.2.4 by running the following command:

conda install -c conda-forge pyside=1.2.4

PySide 1.2.2 is not available on conda but is available via pip.

If you don't see your operating system listed or if the recommended version does not work for your system, please try each version listed to see which works and email the result to hparks@lbl.gov so I can add it to the above list.