Hypertext Atlas For Pathology Education

Josef Feit$^{\dag }$, Luděk Matyska$^{\ddag }$

$^{\dag }$2nd Department of Pathology, Medical Faculty
$^{\ddag }$Faculty of Informatics

Masaryk University, Brno, Czech Republic

Introduction

Microscopic pictures play the key role in pathology diagnosis and education. Collections of histological pictures in printed form are the most common source of reference for pathologists. The goal of this study was to prepare a collection of digital images in the highest quality possible and to provide such a user interface, that would challenge traditional sources of information.

The atlas should have contained text with the table of contents and index, pictures with arrows showing important features. No special software or hardware should have been necessary to use the atlas.

Methods

Pictures are the most important part of this application. Leica DMLB microscope with a set of HC Fluotar lenses equipped with the Leica S1 scanning camera is used to obtain pictures at the resolution of up to 5112 x 5112 pixels, 3 x 12 bit color.

These pictures are digitally manipulated (color balancing, contrast enhancement and sharpening), downsized to 3000 x 3000 pixels, 3 x 8 bit color and archived on CD ROM. Subsequently these images are downsized and compressed using JPEG (JFIF lossy format) to 900 x 900 and 2000 x 2000 pixel images and integrated into the hypertext atlas. Low compression (coefficient of jpeg quality was set to 9) was used, so that the mean size of a 900 x 900 px picture is about 1 MB. Large images are up to 2.5 MB in size.

Pictures are logically put together and described in the atlas source text prepared using the TEX/L^ATEX typesetting system. L^ATEX2HTML convertor is used to produce the actual hypermedia document, while the same source can be used to obtain a printed version of the atlas. This one source philosophy is important for efficiency of source code preparation. Hypertext source for the Internet Browsers is therefore automatically generated, including hypertext links in the table of contents, subchapters, index, in-text cross references etc.

From various techniques available the HTML, JavaScript and to some extent css styles were used; serverside programming and CGI techniques were avoided. The atlas is therefore available on the Internet and on CD as well and no special server is necessary.

User's interface

To demonstrate the user's interface we will look at the screendumps of the system running Netscape and X-Window under Linux operating system. Functioning under MS Windows 95, 98 and NT and MSIE is quite similar.

introductory window

table of contents

text of the atlas with hypertext links to the pictures

secondary window with the picture 900 x 900 px in size is opened, so that the text of the atlas is always available

arrows and text can be activated

It is important to enable using the atlas even in lower bandwith condition. Therefore two sets of images were prepared: 900 x 900 px showing the whole image. In monitors with lower resolution is the size automatically adjusted. If required another, this time fixed size window 400 x 400 px is opened showing part of the large, 2000 x 2000 px picture. This detail showing window scrolls according to the user clicking on the overview window, mimicking magnifying glass efect. This is achieved by JavaScript event catching, appropriate coordinate transformation and window scrolling.

more than one picture window can be open at the same time, each with its own magnifying glass. This enables easy comparing images of different magnifications, stainings etc. However, no more than one magnifying glass can be used on a particular picture.

Another important feature is the possibility of having images taken in several focusing planes. Again through JavaScript controlled image switching the user can mimick focusing the microscope by clicking the buttons. This feature is important especially in high magnifications, where the depth of focus is lower than thickness of the tissue slice.

Discussion

The atlas was primary produced as a stand-alone package, stored on a local disc or CD-ROM. In this form it is suitable for pregraduate and initial postgraduate education. The Internet accessible atlas can be easily updated and expanded with new images and text.

Through the very high speed network (eg. TEN-155) it is possible to transfer even the raw data images with resolution above 3000 x 3000 pixels or three dimensional blocks of images obtained in various focusing planes.

Two images collections are available: skin histopathology (about 300 pictures) and gastrointestinal histopathology (about 80 pictures).

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