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
2. 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
3. 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
4. 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.