TomoBank

Warning

updated June 30, 2020. The server hosting tomobank (petrel) is currently down. The ALCF operations team has completed restoring the data and several files have been identified as possibly being corrupted. We are currently evaluateing each of these files to determine if they are “ok”

If not, we have 2 backup copies of tomobank data on non-spinning disks and we will be able to recover any damaged file. Please check back here for updates.

project

The X-ray Tomography Data Bank or TomoBank, provides a repository of experimental and simulated data sets with the aim to foster collaboration among computational scientists, beamline scientists and experimentalists, to accelerate the development of tomographic reconstruction and 3D visualization methods and to speed up their implementation in the various synchrotron facility data analysis software packages.

If you use the tomoBank Toolbox for your research, we would appreciate it if you would refer to the following papers [decarlo:01]:

De Carlo, Francesco, et al. “TomoBank: a tomographic data repository for computational x-ray science.” Measurement Science and Technology 29.3 (2018): 034004. http://www.doi.org/10.1088/1361-6501/aa9c19

TomoBank relies on Petrel [petrel:19], a resource of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.

Features

  • Tomographic datasets and phantom repository Globus
  • Python scripts to read and reconstruct all data sets (tomopy_rec.py)

Usage:

python tomopy_rec.py -h
    usage: tomopy_rec.py [-h] [--axis [AXIS]] [--type [TYPE]] [--nsino [NSINO]]
                 fname

    positional arguments:
            fname            file name of a tomographic dataset: /data/sample.h5

    optional arguments:
            -h, --help       show this help message and exit
            --axis [AXIS]    rotation axis location: 1024.0 (default 1024.0)
            --type [TYPE]    reconstruction type: full (default slice)
            --nsino [NSINO]  location of the sinogram used by slice reconstruction (0
                             top, 1 bottom): 0.5 (default 0.5)

Example:

python tomopy_rec.py /tomobank/tomo_00001.h5 --axis 1024