Example a/visiblehuman: Visiblehuman: Digitising Visible Human Data

This examples describes how to digitise images from the Visible Human Project using the CMISS digitiser.

A copy of the images from Visible Human Project is currently stored on the main server and is accessible at /people/visible_human/

It is recommended that the images in the "uncropped" directory are used for most cases.

Processing the images

The first step in digitising the images is selected your images and placing them in three-dimensional space. This is can be acheived via the crop.pl script. This script will create a subset version of the dataset according to parameters at the top of this script (these should be changed to suit an individual project's needs). The cropped images should be stored on the local disk to again reduce network traffic.

NOTE: This script requires the ImageMagick perl modules installed on your local machine.

Digitising the images

The second step is digitising the processed image. The "draw.com" can be modified to suit individual projects. Of particular interest may be the variable "%groups" which is a hash of the regions of interest along with the colour which the digitised points will be displayed. After that run "cmgui draw" to begin digitising.

The digitisation environment consists of:

After digitising, the groups may be broken into individual groups by running the splitExdata subroutine (last line of the comfile).

NOTE: This script requires the Gtk perl modules installed on your local machine.

Screenshot of example a/visiblehuman

The comfile run by this example is as follows:


use CmUtils::Digitise qw( cmguiInit checkImageSet setDataGroups loadExdataGroup digitiseSlices splitExdata setGlyphs);
use CmUtils::Digitise::Echo qw( Echo_CreateImageSet );

# Variables user should change

# Default glyph values:
$glyphType = "sphere";
$glyphSize = 3;

$datafile = "traces";
%groups = qw(epi red stomach blue fat green muscle muscle skin tissue );
@groupnames = keys %groups;

# Cmgui 2d digitizer window size
$WinWidth2d    = 800;
$WinHeight2d   = 800;

# Set this to create a 3D data window
$View3d        = 1;

# Cmgui 3d data point viewer window size
$WinWidth3d    = 500;
$WinHeight3d   = 500;

# Set the scale on the viewing window
$CmUtils::ViewNormal::Scale = 150;
$CmUtils::ViewNormal::ViewRange = 4;

$CmUtils::Digitise::settings{max_load} = 5;
$CmUtils::Digitise::settings{saveall} = $datafile;

$images = Echo_CreateImageSet("$example/images/", '.jpg', 'VM');
checkImageSet( $images );

&cmguiInit( $WinWidth2d, $WinHeight2d, $View3d, $WinWidth3d, $WinHeight3d );

# Use setGlyphs if you want to change the default glyph (sphere of size 3)

setDataGroups( %groups );

loadExdataGroup( $datafile, $images );

digitiseSlices( $images );

# splitExdata ( $datafile, @groupnames )

Files used by this example are:

Name              Modified     Size

visiblehuman.com 17-Mar-2014 1.3k COPYRIGHT 17-Mar-2014 504 crop.pl 17-Mar-2014 8.4k images/ 18-Mar-2014 -

Download the entire example:

Name                            Modified     Size

examples_a_visiblehuman.tar.gz 09-Mar-2016 1.8M

Html last generated: Wed Mar 9 16:02:57 2016

Input last modified: Wed Mar 9 15:49:32 2016

CMISS Help / Examples / a / visiblehuman