[MINC-users] img2mnc

[Andrew Janke]

Hi all,

Those who deal with histology data will likely be interested in this:

https://github.com/BIC-MNI/minc-widgets/blob/master/img2mnc/img2mnc

It's part of minc-toolkit so you should see the updates when Vladimir
releases a new version.NAME
       img2mnc - convert an image (PNG, JPG, etc) to MINC

a


$ img2mnc -man
IMG2MNC(1)            User Contributed Perl Documentation           IMG2MNC(1)

NAME
       img2mnc - convert an image (PNG, JPG, etc) to MINC

SYNOPSIS
       img2mnc [options] <infile1.{png|jpg|tif|gif}> [<infile2.png>]
<outfile.mnc>

       img2mnc takes an input image (any format readable by
imagemagick) and converts it to MINC

DESCRIPTION
       img2mnc arose out of the need from converting multiple
histology formats to MINC. This is fine for the major formats but you
often have
       to deal with data in common tif, jpg or PNG form.

       img2mnc will attempt to deduce the step sizes from the input
files based upon their resolution but this is not always correct. If
this
       turns out to be incorrect you will need to correct this later
using mincedit or minc_modify_header.

       Typical usage example for a single input file:

           $ img2mnc in.png out.mnc

       Typical usage for an input set of RGB files with a bitdepth of
16 (unsigned short)

           $ img2mnc -rgb input???.png out.mnc

OPTIONS
       -v, --verbose
           Be noisy when doing things (most importantly this will echo
the resulting script to the terminal)

       --version
           Print version number and exit

       -c, --clobber
           Overwrite existing files

       -h, --help
           Dump some quick help output

       --man
           Dump a man page

       -f, --fake
           Do a dry run. This is usually only useful if combined with
--verbose so that you can see what is going on.

       -t, --tmpdir
           Define a tmpdir in which to place temporary files while processing

       --keeptmp
           Don't remove the tmpdir when complete (usefull for debugging)

       --filelist
           Specify a file that contains a list of input filenames
instead of using those from the command line

       --slice_step
           Specify a slice spacing, this is typically the Z dimension

       --slice_start
           Specify a slice start, this is typically the Z dimension

       --rgb
           Convert the data as RGB resulting in a 4D file

       --depth
           Convert the data at the desired bitdepth. Currently only 8
(byte) and 16 (unsigned short) are supported.

AUTHOR
       Problems or Comments to: Andrew Janke - a.janke at gmail.com