e2proc3d

Generic 3-D image processing program. The main tasks this program can be used for are:

Convert volumes from one format to another
Perform basic image processing operations such as filters, masks, normalization, etc.
Resize/rescale volumes
Compute FSC curves, structure factors, etc.

This program operates on single 3-D image files and EMAN2 BDB databases. While it is possible to put multiple volumes into a single file akin to 2-D particle stacks, it is not widely supported, so this is not a commonly used capability. It has many command-line options for specific tasks. The generic '--process' option is by far the most powerful, offering access to 180+ different image processing operations (for a list, type e2help.py processors).

For specific details on various options, use e2proc3d.py --help.

Examples

convert SPIDER format test.spi to HDF format:

e2proc3d.py test.spi test.hdf

extract a volume from a BDB database and convert to HDF format for visualization in Chimera

e2proc3d.py bdb:refine_01#threed_filt_04 volume.hdf

apply a 10 A low-pass filter to a volume in-place.

e2proc3d.py bdb:refine_01#threed_filt_04 bdb:refine_01#threed_filt_04 --process=filter.lowpass.gauss:cutoff_freq=0.1