How to create snapshots of your Mnc and Obj files

This page describes some tricks you can use to create snapshots of your .mnc and .obj files.

Basic Snapshot in Perl

system(“mincpik -clobber -slice 35 -lookup ‘-hotmetal’ -image_range 0 50 ${input} $output.png”);

Quick way to get snapshots from the command line:

find . -name “*.mnc.gz” -exec mincpik -slice 75 {} {}.png \;


  1. Convert your image to a a grey scale rgb file. Play with the range to get the right contrast.

minclookup -clobber -range 0 500 -grey t1p.mnc t1p_grey_rgb.mnc

  1. Convert your mask to a RED rgb file

minclookup -clobber -lut_string ‘0 0 0 0;1 1 0 0′ mask.mnc mask_red_rgb.mnc

  1. average the two rgb files. The weighting will give you the desired transparency level

mincaverage -clobber -weights “0.1,1″ mask_red_rgb.mnc t1p_grey_rgb.mnc avg.mnc

  1. take a snapshot of the file using mincpik

mincpik -slice 30 avg.mnc snapshot.png

Framing your snapshots

If you want to only take a picture of a certain area, you can use mincreshpae to first crop your image before using mincpik

mincreshape -dimrange xspace=40,177 -dimrange yspace=30,212 in.mnc.gz out.mnc

Note: xspace=start,length


You can use montage to combine multiple png files

montage -tile 2×1 right.png left.png both.png


You can use convert to create a gif animation #Get two or more images using mincpik e.g. to create an animation with a 1 second delay between images, and will loop 4 times

convert -loop 4 -delay 100 out1.png out2.png animation.gif

Please also see the man pages for minclookup, convert, mincpik, mincaverage and montage.