Image information

Header information

Bsoft is capable of reading many different image formats, each with its own header information. Internally, this is translated into a structure common to all images. To display this information, many programs reading images will display image header information when the -verbose option is set to a value that includes the third last bit (i.e. 4: use -verbose 4 or -verbose 7):

bhead -verbose 7

Some of the header information is associated with individual sub-images in the file. To display this information, use the -information option:

bhead -verbose 7 -info

The header information can also be modified in various ways. The following changes the unit cell parameters in the image header (note: if the second file name is the same as the first, the original file is overwritten):

bhead -verbose 7 -unitcell 42.5,60,125.7,90,120,45 2omf.grd test.mrc

For some image formats (such as MRC) many other software packages confuse the semantic difference between 2D images and slices of a 3D volume. This should be corrected in images used in Bsoft. To convert slices of a volume into 2D images:

bhead -verbose 7 -images 2omf.mrc 2omf.mrc

To convert a set of 2D images into a volume:

bhead -verbose 7 -slices 2omf.mrc 2omf.mrc

Statistics and background

A good software package should write the appropriate header information into the file based on a published specification. However, often good practice is not observed and the image file contains strange information. The statistics of the image file can be recalculated:

bhead -verbose 7 -recalc 2omf.mrc 2omf.mrc

Similarly, the background (the area outside the oval/ovoid inscribed within the image) can be calculated and masked or subtracted with various options. To calculate and mask it:>/p:

bhead -verbose 7 -Back 2omf.mrc 2omf_bkg.mrc


The histogram of an image and information content associated with it can be calculated over a given number of bins and output to a postscript file:

bhisto -verb 7 -bins 200 -Post 2omf.grd


All Bsoft programs write text labels into the image headers. Most of these are the command lines used to generate those files. One can therefore always backtrack the sequence of processing done on a set of images (of course providing that intermediates have not been deleted).

Concatenating and splitting files

Multiple image files can be concatenated into one file as multiple images or as slices of a 3D image:

bcat -verbose 7 -output file.mrc in*.map

Similarly, image files can be split into their sub-images or into individual slices of a 3D volume:

bsplit -verbose 7 file.mrc