AnatLab Project

ANATLAB VIRTUAL ANATOMY LABORATORY

The AnatLab Virtual Anatomy Laboratory was developed for NMHM Chicago by Tyler, Texas-based Eolas Technologies Inc., its subsidiary, Iomas Research, and with consultants Dr. Maurice Pescitelli, Steve Landers, and Steve Huntley. AnatLab allows users to navigate through all areas of the body and investigate any section in detail with the click of a mouse. When objects are identified and highlighted by a user, web links are provided for more detailed information on the structures. A search bar enables users to search for any structure within the body which can then be viewed in an axial, sagittal, or coronal view.

 

Visible Human Male Database

Leveraging the data sets from the National Library of Medicine's Visible Human Male, the AnatLab system acts as a navigator allowing users to explore the human body. This data set includes a series of 1,871 anatomical images which each represent 1mm axial color cross sections through a male cadaver.

 

Annotation Tools & Imagemap Processing

The AnatLab annotator is a Tk-based graphical annotation tool used by anatomical experts to define the boundaries of structures on each section in the Visible Human data set.

During the annotation process, the user (i.e. the anatomy expert) chooses an anatomical object name and identifies the object by drawing polygons on magnified cross-sectional images. The polygons can comprise multiple line segments or smoothed splines and can be edited, copied, and pasted to other sectional images.

 

Zmap Technology

The polygonal data from the annotation tools is used to generate secondary maps of 24-bit color “indices” where a given x,y,z coordinate in the original image data corresponds to an homologous x,y,z location in the secondary “map” of 24-bit voxels. The RGB triplet found at that location in the secondary map then acts as a unique 24-bit object index for the image feature in the original data. Once integrated, the system can then perform database table lookups for that 24-bit index in order to find the related semantic data.

 

Coronal & Sagittal Section Generation

Utilities from the Netpbm toolset coordinated by a Tcl script were used. GNU make was used for parallel processing. The steps are outlined below:

・decompress the axial section image files

・assign each raster line of the images to individual files

・re-assemble the rasters in new configures to produce contiguous image files in the desired orientations

・re-translating the resulting image files to JPEG format

 

Overlay Generation

Overlay generation is accomplished by a combination of Netpbm utilities and makefiles controlled by Tcl scripts. For each imagemap, a list of unique 24-bit color indexes is extracted. A color mask for each anatomical object is generated, then the color mask is overlaid onto the corresponding section image file, resulting in a new file containing only the image area of the anatomical object. The overlay image is tinted to provide a highlight effect when displayed over the section image in a Web browser.

 

Wikipedia links

A click on the “more...” link will open a second window with the Wikipedia entity for that structure. As the user clicks on other structures in the atlas, the Wikipedia window stays in sync, showing each structure's information.

 

"AnatLab: A Web-based Virtual Anatomy Laboratory" presented at the 15th Annual Tcl/Tk Conference in Manassas, VA  October 20-24, 2008

"The use of Tcl/Tk in the AnatLab Virtual Anatomy Laboratory" presented at 16'th Annual Tcl Association Tcl/Tk Conference in Portland, OR  September 28-October 2, 2009