HCIL Visible Human Explorer Help

Human-Computer Interaction Laboratory,
University of Maryland at College Park

The Visible Human Explorer Main Window:

The Visible Human Human Explorer prototype allows you to browse a miniature overview volume of the National Library of Medicine's Visible Human data set, and retrieve high-resolution images over the internet from the NLM VHP archive on demand.

Browse the data set by simply dragging the yellow slider line in the Overview box. The view in the Image Select box displays the axial cross-section corresponding to the Overview slider position. Likewise, drag the slider in the Image Select box to explore new coronal section overviews. Press the icon buttons on the left of the overview image for several different overview perspectives.

To view the high-resolution image of the axial cross-section shown in the Image Select box, press the "Retrieve Full-Size Image" button. You may download the image over the internet from the NLM archive or, if you have already done so, display your local copy. See the Retrieve Full-Size Image dialog box section below.

To download an entire contiguous range of images, for example, all images between slice 1401 and 1475, use the Range Select box. To do this, move the overview slider to the top of the range, slice 1401, and press the Top image button in the Range Select box. Then move the oveview slider to the bottom of the range, slice 1475, and press the Bottom image button in the Range Select box. Then press the "Retrieve Full-Size Images" button in the Range Select Box. Be careful, you may find yourself downloading 500 MB of data!

In the text box below the overview image, enter the name of your local image directory and press the Return key. Tick marks on the vertical black bar next to the overview image indicate high-resolution axial images which have already been downloaded to that local directory. Place the yellow overview slider line on top of a tick mark, and a the word "Local" appears in the Image Select view. Press the Retrieve button, then the Display Local Image button.

The Retrieve Full-Size Image Dialog Box:

The "Retrieve Full-Size Image" dialog box downloads images over the internet from the NLM VHP image archive and displays them.

Access to the National Library of Medicine's Visible Human Project image archives requires a license agreement with NLM. For more information, consult the NLM VHP web site at: http:/ /www.nlm.nih.gov/research/visible/visible_human.html

To download remote images, supply information for each field including your NLM archive Login ID and Password obtained from the NLM License Agreement. The other fields are already filled in based on information from the VHE Main Window. Then press "Retrieve Remote Image". The progress meter will show the status of the retrieval process. Press "Abort" to stop the retrieval at any time if needed. Then, to display the image once it is downloaded, press "Display Local Image". Images may take a minute to display.

Similarly, to display an image that you have downloaded previously, just press "Display Local Image". You do not need to wait for the download time, only the display time.

To view CT Scan images, select the "CT Scan" toggle on and turn off the "Color Cryosection" toggle. Then, retrievals and displayings will use CT images instead of the color images.

Pressing "Save Settings" will save the current settings (Login ID, Password, VHP Host, Local Image Directory, and state of the Color and CT toggles) as the default values.

This dialog box will not dismiss until you press the Close button.

Full-Size Image Display:

This is a standard full-featured image display and editing tool, not built by us. See its help documentation for more information. Press the right mouse button inside the image to show its dialog box. Press the Quit button in that dialog to exit the image display.

VHE Trouble Shooting:

The program does not run or crashes? Be sure all the VHE data and executable files are in one directory. You must run "vhe" from within that directory. i.e. "cd" into that directory, then type "vhe" to run it (or type"./vhe" if needed). Also, try typing "setenv DISPLAY :0.0", then "vhe". Some have also found that running the SunOS version on Solaris machines works better.

High-Resolution images won't download from NLM? Make sure that typing "ftp" starts the ftp command line (type "quit" to exit it). If not, check with your system administrator. Also make sure you have entered your Visible Human login ID and password (from the NLM License Agreement) correctly in the Retrieve dialog box.

High-resolution images won't display? Make sure you have the standard image display program called "xv". If typing "xv" does not start that program, then ask your system administrator about getting that program or see the Hackers' Notes below about using other image display programs.

Also, the high-resolution images are very large, and may take several minutes to display on slower machines. Be patient. Older machines will get bogged down if you try to display too many of these images!

If the program continues to crash or misbehave, please send a bug report to north@cs.umd.edu describing the problem, error messages, and output of "uname -a".

VHE Experienced Hackers' Notes:

The "vhe" program must be run from within the directory containing the VHE data and binaries. To be able to run it from elsewhere, write a shell-script (or alias) that does something like:

  cd your-vhe-directory
  vhe &

If your site has its own complex archive for the full-res data, or you use some other image format, or you wish to use some other applications for viewing/manipulating images, you may change the actions of the interface buttons as follows:

To make the "Retrieve Full-Size Image" buttons on the main VHE window do something different, simply replace the "vhftp" program with some other program or shell-script. The calling arguments are:

  vhftp slice#[-toSlice#] localDirName

The "Display Local Image" button in the Retrieve dialog box uses unix "uncompress" and the supplied "vhRawToPpm" or "vhCatToPpm" programs to convert the compressed raw/CT image to a ppm image, then uses the standard image display program "xv" to display it. To change the action of this button, write a shell-script called "xv" and put in the directory with the vhe program. Make sure "." is in your $path environment/shell variable before the directory containing the real "xv". The calling arguments are:

  xv localDir/a_vm####.ppm         (for color cryosection images)
  xv localDir/c_vm####.fro.ppm     (for CaT Scan images)

Replace the "vhRawToPpm" or "vhCatToPpm" to generate some other image format. Its calling sequence is:

  vhRawToPpm localDir/a_vm####.raw localDir/a_vm####.ppm        (color cryos)
  vhCatToPpm localDir/c_vm####.fro localDir/c_vm####.fro.ppm    (CaT Scans)

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