cryohub

cryohub is a library for reading and writing Cryo-ET data based on the cryotypes specification.

Installation

pip install cryohub

Usage

cryohub provides granular I/O functions such as read_star and read_mrc, which will all return objects following the cryotypes specification. A higher level function called read adds some magic to the IO procedure, guessing file formats and returning a list of cryotypes.

Similarly to the read_* functions, cryohub provides a series of write_* functions.

From the command line

If you just need to quickly inspect your data, this command will land in an ipython shell with the loaded data collected in a list called data:

cryohub path/to/files/* /other/path/to/file.star

Features

Currently cryohub is capable of reading images in the following formats:

• .mrc (and the .mrcs or .st variants)
• Dynamo .em
• EMAN2 .hdf

and particle data in the following formats:

• Relion .star
• Dynamo .tbl
• Cryolo .cbox and .box

Writer functions currently exist for:

• .mrc
• EMAN2 .hdf
• Dynamo .em
• Relion .star
• Dynamo .tbl

Image data

When possible (and unless disabled), cryohub loads images lazily using dask. The resulting objects can be treated as normal numpy array, except one needs to call array.compute() to apply any pending operations and return the result.

Contributing

Contributions are more than welcome! If there is a file format that you wish were supported in reading or writing, simply open an issue about it pointing to the specification. Alternatively, feel free to open a PR with your proposed implementation; you can look at the existing functions for inspiration.