How to create snapshots of your Mnc and Obj files

General HowTo
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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 \;

Transparencies

  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

Montages

You can use montage to combine multiple png files

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

Animations

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.