LIFE SCIENCES VIEWING ROOM

Bart M. ter Haar Romeny

, Mark (L. C. M.) Bruurmijn

, Laurens E. O. Leeuwis

and Y. Kang

Department of Biomedical Engineering, Eindhoven University of Technology

Den Dolech 2, 5612 AZ, Eindhoven, The Netherlands

Sino-Dutch Biomedical and Information Engineering School of Northeastern University

11-3 Lane, WenHua Road, Shenyang, China

Keywords: Medical images, PACS, Life sciences, 3D viewing, Reading room, Education.

Abstract: A radiological picture archiving and communication system (PACS) has been installed at the department of

Biomedical Engineering of TU/e for student and researchers use. The availability of large sets of high

resolution 3D image data sets, and the extensive interactive 3D manipulation possibilities, turn out to be an

important support and stimulation for the students in their projects. The system can be considered an

ultimate interactive 3D anatomy book.

1 INTRODUCTION

Medical images play a crucial role in the diagnostic

process. It is estimated that 80% of all diagnoses are

done based on images. They are made in huge

numbers, with a wide variety of medical imaging

devices, such as X-ray systems, CT and MRI

scanners, ultrasound systems, PET scanners, etc.

Almost every modern hospital is now equipped with

a medical image database, accessible from a large

number of places throughout the hospital. Such a

system is called ‘Picture Archiving and

Communication System’ (PACS) (Huang 2010).

Typically it contains several tens of terabytes of

information, and has now fully replaced the film-

based archive and viewing.

Viewing (also called ‘reading’) of the images, in

order to do the diagnosis, and comparing the current

exam with previous ones, is typically done in a

‘reading room’ (figure 1), on a PACS viewing

system. Such a system is not only capable of

browsing quickly in the database and retrieve the

image data, but also has a wide range of additional

functions, such as interactive 3D viewing, slicing of

3D data in any direction, automated detection of

anomalies such as polyps, narrowed bloodvessels

(stenosis), diminished perfusion, etc. (Beutel et al.

2000]. Modern medical image analysis software is

able to perform these tasks (ter Haar Romeny 2007,

Fitzpatrick 2009). The field of ‘computer-aided

detection and diagnosis’ is rapidly evolving. PACS

has a positive influence on the education of

radiologists in training (Mullins et al. 2001). At

technical universities, where students are trained to

become a specialist / engineer in medical image

analysis, such valuable patient datasets are often not

available, or only in limited numbers and types.

Figure 1: Reading room at a radiology department.

445

M. ter Haar Romeny B., (L. C. M.) Bruurmijn M., E. O. Leeuwis L. and Kang Y..

LIFE SCIENCES VIEWING ROOM.

DOI: 10.5220/0003353704450448

In Proceedings of the 3rd International Conference on Computer Supported Education (CSEDU-2011), pages 445-448

ISBN: 978-989-8425-49-2

 2011 SCITEPRESS (Science and Technology Publications, Lda.)

We installed a PACS for student use at the

Biomedical Engineering Department of Eindhoven

University of Technology, the Netherlands. This

system contains an exhaustively complete set of

anonymized high resolution 2D and 3D medical

imaging datasets of a wide range of modalities,

primarily of normal subjects. The system has a fast

GPU based 3D viewing mode for huge datasets. As

such, it forms a rather unique, fully interactive

anatomy book.

2 LIFE SCIENCES VIEWING

ROOM

The acquisition of two PACS workstations from the

company Rogan Delft is made possible by a

generous gift of the Eindhoven University Fund

(UFE). These two workstations, communicating

over a gigabit network with a 1 TB server-side

database, are set up in the so called Life Sciences

Viewing Room, which is given a prominent place in

the department. Both workstations consist of a

powerful pc with 4 GB RAM and an NVidia GTX

8800 graphics card (GPU). The data can be viewed

using three professional Eizo medical displays: two

Radiforce G22 monitors (black-and-white, 10 bit

colordepth, 2 megapixel) and one Radiforce R22

color display.

Figure 2: 3D view of the carotid arteries with severe

stenosis. CT data. Courtesy: 3mensio Inc.

The high graphical performance of the workstations

allows software like 3viseon by the Dutch company

3mensio Medical Imaging BV to render astounding

volumes in real time on the GPU (Figure 2). This

adds a very special dimension to the system. The

students can interactively inspect any anatomical

part of the body, be it from CT or MRI data, zoom,

rotate, cut away views, fly through intestines or

blood vessels, do measurements, and act just like a

professional radiologist during his careful inspection

of the data. The system is also equipped with extra

software for grabbing movies of any screen action,

enabling the student to make promotional material

for his project presentation, or show these proudly at

home.

The two systems are located in the experimental lab

of the department, and are fulltime accessible. For

one of the systems a dedicated room is constructed

with dimmable lighting, and theatre sitting for 16

people, for discussions and presentations.

The medical 2D and 3D datasets are collected

from collaborating hospitals and industry, and from

general accessible databases on the internet,. The

system may currently be one of the most complete

interactive anatomy books around. The available

data are mostly of normals, with some pathology.

This serves the purpose of general viewing for the

students. If a project is done on e.g. heart valves,

these can be studied interactively and in full detail in

3D on the system. Next to medical data the system is

now filled with images from the life sciences—the

reason why the facility is calles Life Sciences

Viewing Room—such as microscopy from a wide

range of microscopes available in the Biomedical

Engineering Department (conventional light,

confocal, and 2-photon scanned laser microscopes),

and high field (6-9 Tesla) small bore MRI systems

for small animal imaging.

Two student assistants are appointed to fill the

system with relevant high resolution, high quality

data. The system now has a rather complete set of

anatomical areas, with many modalities, and is

growing. About 250 datasets are currently available.

The book Gray’s Anatomy is located on the user’s

desk for reference. The graphical user interface

(GUI, Figure 4) of the system is designed by these

assistants, enabling a first graphical selection on

anatomical region, then modality, then a specific

patient, and finally a specific dataset of that patient.

All data are in the standard DICOM format (DICOM

– Digital Imaging and Communications in Medicine,

a universal standard adopted by the medical imaging

industry and community), and have been carefully

anonymized. To further prevent any chance of

recognizing the face of a patient, We exchange data

with a similar database in our sister BMIE School in

Shenyang, China. There, the 3D viewing and

manipulation software is based on the PACS viewer

of Neusoft Inc.

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446

Figure 3: Students active with the casus to analyse micro-

scopy images of blood cells for pathology.

3 ROLE IN EDUCATION

The system can be accessed at all times by all

students. It is however also part of the regular

curriculum. Two courses exploit the new interactive

viewing capabilities. During the so-called Skills-

Labs, at the end of the last year of the Bachelor

curriculum, the students have to generate

demonstration movies of 3D manipulation of a

specific and specified anatomical region, answering

specific question about the 3D anatomy such as

‘where exactly is the polyp located’, ‘what is the

shortest distance of the kidney surface to the skin’,

‘what is the diameter of the carotid artery just above

the bifurcation’. Students work in pairs during these

labs.

A second course is a so-called casus, a first-year

BSc project of six weeks for groups of eight students

(Figure 3), entitled Image Processing for Pathology.

In this casus students build an automated system to

assist the pathologist to analyze cells from

microscopy images. They need to ‘find the sick cells

among the healthy ones’. They are free in the

selection of the type of disease, type of images, and

task to solve. An interesting spirit of competition

emerges between the typically 8-10 groups of

students simultaneously active. The cell analysis

software is developed in Wolfram’s Mathematica 7.

The Life Sciences Viewing Room facility is used

to view and inspect the data, and to run a dedicated

program (Huygens, by SVI Inc.) to sharpen the

microscopy images by deconvolution. The actual

working and experimenting with this program gives

Figure 4: User interface with thumbnails to quickly select

a particular 3D dataset.

them a much better understanding of the underlying

theoretical principles of deconvolution, which are

non-trivial for most students.

In our sister BMIE school in Shenyang, China,

we have set up a new curriculum with emphasis on

Design Centered learning. We foresee that their

copy of the Life Sciences Viewing Room will enable

the same ‘explorative urge’ of the students, and

facilitate the use of extended datasets in current

projects of research on image analysis and

visualization.

4 DISCUSSION

The system is much appreciated by the students.

Besides the already developed virtual anatomy book,

the ambition is to have the Life Sciences Viewing

Room grown into a pivot of biomedical images for

the faculty, containing images from all research

areas in the department, which can be used for

various educational goals. It also turns out to have

an attractive role in demonstrations of the current

status in biomedical imaging, for visiting parents

and new employees alike.

This system is easy to build, and might benefit of

joining a network of users, who each supply new

LIFE SCIENCES VIEWING ROOM

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and additional datasets in a shared database to each

other. For patient security, care should be taken to

properly anonymize all data, to prevent any chance

of recognition. Students appreciate the ‘playing with

data’, are introduced to the many sophisticated

viewing applications, and embrace it as an exciting

new tool for fast and visual image manipulation and

analysis, be it for medical or life sciences data.

ACKNOWLEDGEMENTS

We like to thank the sponsors of the PACS system,

Rogan Delft BV, Organon, Unilever, 3mensio Medi-

cal Imaging, the TU/e BME department and Olym-

pus ‘58 en ‘74/ESC, and Neusoft Medical Systems

Inc. for the availability of the 3D PACS viewing

software.

REFERENCES

PACS:http://en.wikipedia.org/wiki/Picture_archiving_and

_communication_system

Beutel, J., Kim, Y., Display and PACS, SPIE Press, 2000.

DICOM standard: http://medical.nema.org/.

Fitzpatrick J. M., Sonka M., Handbook of Medical

Imaging, Volume 2. Medical Image Processing and

Analysis. SPIE Press Monograph Vol. PM80/SC,

2009.

Huang, H. K., PACS and Imaging Informatics: Basic

Principles and Applications. John Wiley and Sons,

2010.

Mullins ME, Mehta A, Patel H, McLoud TC, Novelline

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residents: the residents' perspective. Acad Radiol.

8(1):67-73, 2001.

Rogan PACS viewing software: http://www.ncdcorp.com/

vpx_viewer.php

Silva-Lopes, V. W., Monteiro-Leal, L. H., Creating a

Histology–Embryology Free Digital Image Database

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Anatomical Record (part B: New Anat.) 273B:

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ter Haar Romeny, B. M., Image Processing on Diagnostic

Workstations, in: Image Processing in Radiology,

Current Applications (E. Neri, D. Caramella, C.

Bartoluzzi, Eds.), Springer Verlag, 2007.

Website Life Sciences Viewing Room: http://bmia.bm

t.tue.nl/lsvr.

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