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 3.11 and newer 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
packaging
blosc (optional, but highly recommended)
blosc2 (optional)
Compression backends
The two bindings are not interchangeable, because they emit different chunk formats:
blosc (c-blosc1) writes version-2 chunks, the only ones older mrcz can read. It is the write default, so install it if anything else must read your files.
blosc2 (c-blosc2) reads both formats, so it is preferred for reading. It writes version-5 chunks, used only when asked for, when a blosc2-only codec is requested, or when blosc is absent.
Installing neither disables compression; uncompressed MRC still works.
Pass backend='blosc2' to opt in to version-5 chunks:
mrcz.writeMRC(image, 'out.mrcz', compressor='zstd', backend='blosc2')
On read, header['bloscFormat'] reports the format a file actually uses (1 or 2), detected from the chunk rather than a header flag.
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/
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
1 maintainer
Metadata
1 maintainer
Release files for mrcz 0.6.0
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Total release size: 118.1 kB
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