mrcz 0.5.9

MRCZ meta-compressed image file-format library

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 of your Python environment, from a command prompt type:

pip install mrcz

mrcz has the following dependencies:

• numpy

• blosc (optionally, but highly recommended)

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

• R.A. McLeod, R. Diogo-Righetto, A. Stewart, H. Stahlberg, “MRCZ – A file format for cryo-TEM data with fast compression,” Journal of Structural Biology, 201 (3) (March 2018): 252-267, https://doi.org/10.1016/j.jsb.2017.11.012

• 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