Improvements in education in pathology: Virtual 3D specimens

Improvements in education in pathology: Virtual 3D specimens

ARTICLE IN PRESS Pathology – Research and Practice 205 (2009) 811–814 www.elsevier.de/prp ORIGINAL ARTICLE Improvements in education in pathology: ...

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ARTICLE IN PRESS

Pathology – Research and Practice 205 (2009) 811–814 www.elsevier.de/prp

ORIGINAL ARTICLE

Improvements in education in pathology: Virtual 3D specimens Thomas Kalinskia,, Ralf Zwo¨nitzerb, Thomas Jonczyk-Weberc, Harald Hofmannd, Johannes Bernardingb, Albert Roessnera a

Department of Pathology, Otto-von-Guericke-University, Leipziger Str. 44, D-39120 Magdeburg, Germany Department of Biometry and Medical Informatics, Otto-von-Guericke-University, Magdeburg, Germany c Audiovisual Media Center, Otto-von-Guericke-University, Magdeburg, Germany d Medical Computer Center, Otto-von-Guericke-University, Magdeburg, Germany b

Received 15 April 2009; received in revised form 21 April 2009; accepted 27 April 2009

Abstract Virtual three-dimensional (3D) specimens correspond to 3D visualizations of real pathological specimens on a computer display. We describe a simple method for the digitalization of such specimens from high-quality digital images. The images were taken during a whole rotation of a specimen, and merged together into a JPEG2000 multidocument file. The files were made available in the internet (http://patho.med.uni-magdeburg.de/research.shtml) and obtained very positive ratings by medical students. Virtual 3D specimens expand the application of digital techniques in pathology, and will contribute significantly to the successful introduction of knowledge databases and electronic learning platforms. r 2009 Elsevier GmbH. All rights reserved. Keywords: Digital pathology; Virtual 3D specimens; JPEG2000; Education

Introduction Formalin-fixed specimens from organs representing pathological findings are inevitable for teaching medical students in pathology. Therefore, most departments of pathology possess large collections of such specimens, which are exhibited in open large glass-fronted cupboards at best, but which are often concealed from the students in storages or cellars behind closed doors, only available during courses or seminars. Anyway, a permanently accessible exhibition of these specimens would require considerable expenditures and is therefore not reasonable. Moreover, there is an increasing demand for electronic learning (e-learning) using the Corresponding author. Tel.: +49 391 67 17874; fax: +49 391 67 290724.

E-mail address: [email protected] (T. Kalinski). 0344-0338/$ - see front matter r 2009 Elsevier GmbH. All rights reserved. doi:10.1016/j.prp.2009.04.011

internet, which leaves conservative concepts of personal ‘in front’ teaching. Therefore, our intention was to find a solution to digitally present specimens in a way that enables a three-dimensional (3D) impression on the computer display, which gets close to the reality, as simple pictures are not sufficient for this purpose. Recently, we introduced virtual 3D microscopy using JPEG2000 multi-document files enabling digital focusing [1,2], which are suitable for integration in DICOMconform picture archiving and communication systems and pathology information systems [3–5]. Moreover, JPEG2000 allows a data streaming over the internet using JPEG2000 Internet Protocol (JPIP). We presume that such JPEG2000 files are also appropriate for macroscopic images of specimens enabling a zoomable 3D view. Therefore, we constructed JPEG2000 files from high-quality digital images, taken during a whole

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rotation of the specimen. We here present the results and discuss further trends and impacts on teaching and learning in pathology.

Methods Typical formalin-fixed specimens in glassy jars, obtained from the collection of the Department of Pathology, were placed onto a rotatable plate with gauge. Uncompressed digital images were taken using a professional digital camera with a maximum resolution of 12 megapixels fixed on a tripod, while the specimens were rotated in steps of 22.51. Using this angle, 16 images per specimen were taken during one rotation, starting at 01 and finishing at 337.51. From specimens with an opaque back, only 9 images, including views between both sides and the front using the same rotation steps of 22.51 with an overall angle of view of 1801, were taken, starting from the left side of the specimen. Afterwards, the images were processed using Kakadu software, Sydney, Australia (http://www.kakadusoftware.com), according to the manufacturer’s manual. All images of a specimen were merged together into a JPEG2000 multi-document file using a 20:1 lossy compression, constituting a virtual 3D specimen. These virtual specimens were made available in the internet using the AJAX-based web viewer service JPView (Imassense, Berlin, Germany; http://www.imassense.de) running at the Department of Pathology (http:// patho.med.uni-magdeburg.de/research.shtml), enabling scrolling through the multiple views and magnifying details, as in virtual 3D microscopy.

Results An example of the multiple views of a virtual 3D specimen is shown in Fig. 1. It represents a kidney with

granular renal atrophy on the basis of glomerulonephritis. It consists of 16 images taken during the rotation of the specimen in steps of 22.51. The file sizes of the 16 uncompressed images were 31.3 MB each, altogether about 500 MB. The size of the corresponding compressed JPEG2000 multi-document file was 26.1 MB. The 3D effect became evident by scrolling through the multiple views of the virtual specimen. Some images from the edges of the glassy jars showed artifacts, such as reflections and distortions, which were caused by the cuboid form of the jar, not by the digital technique. Due to the varying illumination, details of the granular surface of the kidney were clearly recognizable, especially at higher magnification as shown in Fig. 2. Using magnification, an inspection of the specimen at a distance closer than in reality was possible. This also applied to the file sizes and the quality of other virtual 3D specimens. The medical students’

Fig. 2. Screenshot of the content of the web viewer window showing a magnified detail of the specimen from Fig. 1, with clearly recognizable granular surface of the kidney. The angle of view corresponds to a rotation of the specimen of 22.51 (image 2/16).

Fig. 1. Multiple views (16 images) of the virtual 3D specimen representing a kidney with granular renal atrophy on the basis of glomerulonephritis. The images were taken in high quality during a whole rotation of the specimen in steps of 22.51.

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evaluation regarding applicability, image quality, the ease of use, and the effectiveness of virtual 3D specimens for education in pathology was very positive throughout.

Discussion Virtual 3D specimens provide an opportunity to study real pathological specimens independent of the accessibility to their cabinets. The 3D effect exceeds the limits of conventional macroscopic pictures, and gives rise to a spatial impression. Additional magnification allows a closer inspection of the specimen than in reality. Therefore, virtual 3D specimens at least support education in pathology with some additional value. In our department, the virtual 3D specimens provide the medical students with an additional learning effect, using the same specimens as reviewed in the courses and seminars, and allow for their recapitulation. Anyway, we are convinced that virtual 3D specimens are also adequate for primary reviewing. Certainly, some basic experience with real specimens might be necessary for their proper assessment. Therefore, virtual 3D specimens might not fully replace the review of real specimens or the attendance at postmortem examinations in pathological education. Apart from formalinfixed specimens in glassy jars, other types of specimens can be successfully digitized in a similar way, as demonstrated subsequently by a maceration specimen of the spine with ankylosing spondylitis (Bechterew’s disease). The latter was carried out using a suitable clamping fixture, which may also be necessary for other objects, e.g. unfixed specimens. Particularly, those transient specimens might be preserved with this technique, at least virtually. Apart from the corresponding file sizes, the number of images of virtual 3D specimens is not limited, so that more than 16 views, as suggested here, may be included, if applicable. Images from additional angles of view may also be added, if reasonable. However, the images from the top or from the bottom of the formalin-fixed specimens in glassy jars turned out to be not informative. Nonetheless, additional images might boost the 3D effect, which precisely does not correspond to a real 3D data model with voxels, but certainly corresponds to a 3D visualization using conventional 2D images taken from different perspectives. We believe that real 3D graphics would not increase the informative value of virtual specimens, but would require tremendous technical efforts and expenditures, as a 3D scanner and related hard- and software would be the necessary technical equipment. Real 3D graphics may also be constructed from image series obtained by computed tomography as described for musculosceletal pathology specimens [6]. However, these objects lack photo-realistic impressions,

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which are necessary for the recognition of certain macroscopic findings, particularly regarding colors and structures. Certainly, an additional radiological processing of the specimens would be worthwile for radiopathological correlation teaching. Virtual 3D specimens, as described here, can be prepared using merely standard equipment. JPEG2000 is an appropriate format for this purpose, which enables streaming of the multiple images of the specimen. Moreover, JPEG2000 supersedes JPEG standard by an improved compression performance resulting in fewer compression artifacts. By default, we applied a lossy compression of 20:1 in JPEG2000 format, which has been described to be below a threshold, where recognizable compression artifacts may occur in the form of blurring at high magnifications [4,7]. However, even higher compression ratios may be applicable without any significant influence on the diagnostic accuracy, as proved for virtual 3D microscopy in the diagnosis of Helicobacter gastritis [2]. Although virtual 3D specimens themselves already represent a significant improvement in pathological education similar to virtual microscopy [8–13], the connection to further resources of information will have an enormous impact on education in pathology. Our next intention is to supplement virtual 3D specimens with relevant descriptions of the findings and the disease patterns. Furthermore, several resources of information may be linked with the virtual 3D specimens or vice versa using the internet, constituting a network of pathological information. We presume that the further conjunction of data from different fields of medicine, e.g. the integration of pathological, radiological, and clinical knowledge, will support students in obtaining interdisciplinary skills. Regarding the vast quantity of information, we are convinced that an integrative database related to pathology would be the optimal solution for data mining. For this purpose, we have recently set up an open database on the basis of mediawiki named ‘pathowiki’ (http://www.pathowiki.org or http://de.pathowiki.org) with pending release of an English version, which is bound to be filled with data, including virtual 3D specimens and virtual microscopy. We will introduce this project in a forthcoming report. Altogether, these steps are appropriate to support education in pathology. Furthermore, virtual 3D specimens together with virtual microscopy can also provide the basis for digital teaching using e-learning platforms, such as moodle (http://www.moodle.de). These platforms also permit computer-based proficiency testing, which can supersede the troublesome management of real specimens and/or microscopes in exam situations. As the majority of students insist upon the application of e-learning, such projects are obviously promising investments.

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In summary, virtual 3D specimens expand the application of digital techniques in pathology, and will contribute to the successful introduction of knowledge databases and e-learning platforms for education in pathology.

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