/python-mrcz

Python module for compressed MRCZ-file format

Primary LanguagePythonOtherNOASSERTION

Python MRCZ meta-compressed file-format module

mrcz is a package designed to supplement the venerable MRC image file format with a highly efficient compressed variant, using the blosc meta-compressor library to shrink files on disk and greatly accelerate file input/output for the era of "Big Data" in electron and optical microscopy.

Python versions 2.7, 3.4-3.6 are supported.

mrcz is currently considered to be a beta development state.

mrcz is released under the BSD 3-clause license.

Installation

A scientific Python installation (such as Anaconda, WinPython, or Canopy) is advised. After installation, from a command prompt type:

pip install mrcz

mrcz has the following dependencies:

  • numpy
  • blosc

Feature List

  • Import: DM4, MRC, MRCZ formats
  • Export: MRC, MRCZ formats
  • Compress and bit-shuffle image stacks and volumes with blosc meta-compressor
  • Asynchronous read and write operations.
  • Support in the hyperspy electron microscopy package.

Documentation

Documentation is hosted at http://python-mrcz.readthedocs.io/

Authors

See AUTHORS.txt.

Citations

  • A publication detailing the performance of MRCZ is currently 'in-press'.
  • A. Cheng et al., "MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography", Journal of Structural Biology 192(2): 146-150, November 2015, http://dx.doi.org/10.1016/j.jsb.2015.04.002
  • V. Haenel, "Bloscpack: a compressed lightweight serialization format for numerical data", arXiv:1404.6383