Using this atlas

1  Introduction

1.1  Using this atlas

E-mail of the main author of this atlas:

1.1.1  Conditions of using this atlas

This collection of histological pictures is put on display without any warranty or guarantee of its correctness or usefulness.

You are NOT allowed to copy or download parts of the atlas anywhere, distribute or sell them, using downloading robots, mirror the site or use the pictures, text, logo or design of this atlas in any way without written permission of the authors.

While the information in this atlas is believed to be true, neither the authors, nor the contributors or publisher can accept any legal responsibility for any errors or omissions that may be made. The authors, contributors and publisher make no warranty, expressed or implied, with respect to the material contained herein.

1.1.2  Technical notes  Hardware

Leica DMLB microscope with a set of fluotar lenses (HC Fluotar 5/0.15, 10/0.30, 20/0.50, 40/0.70, 100/1.30 and a Plan 2/0.07 lenses) equipped with the Leica S1 scanning camera is used to obtain pictures at the resolution of up to 5112×5112 pixels, 3×12 bit color.

Later Leica DMLA microscope with a set of PlanApo lenses (HC Fluotar 5/0.15, HC PlanApo 10/0.30, 20/0.50, 40/0.70, 100/1.30 and a Plan 2/0.07 lenses) equipped with the Nikon DMX-1200 digital camera was used to obtain pictures at the resolution at 1200×1000 pixels, 3× 8 bit color. Motorized stage (Merzh√§user) was automatically moved from one image to another. Software for image analysis and manipulation Lucia DI by LIM (Laboratory Imaging, Prague) was used to create composed, very large pictures.

The same microscope and software is now used to create focusable images.

Recently we are using microscope Nikon 90i equipped with a set of objectives 2 – 100×. Objectives CFI PlanApo 20×/0.75, CFI 40×/0.95, CFI VC 60× and CFI VC 100× are used to capture the images. The microscope is controlled by NIS ELEMENTS AR LIM (Laboratory Imaging, Prague). Camera Nikon DS-Fi1 has resolution 2560×1920 px, 3×8 bit. Motorized stage: Prior ProScan with a holder for 4 slides. The system was obtained through grant support MEDIGRID (CESNET) in 2008.

These pictures are digitally manipulated (color balancing, contrast enhancement and sharpening), 3×8 bit color and archived on CD ROM. Subsequently these images are compressed using JPEG (JFIF lossy format) to 900×900 pixel images and integrated into the hypertext atlas. Sizes of very large images (showing details) are up to 7400×7400 pixels.

Images with focusing feature (z-stack of images) were taken by Nikon Eclipse 1000 microscope with a set of Plan Fluor lenses (esp. 100/1.30) with motorized focusing, digital camera 1300×1000 px (Basler), controlled by Lucia DI image analysis (LIM) software.

The same microscope and camera were used to take some of the fluorescence images.  Software
  1. Scanning: Driver for Leica S 1 Camera
  2. Composed pictures: Lucia DI
  3. Automated scanner: Aperio Scanscope 2
  4. Adobe Photoshop 8.0 under Windows XP
  5. Perl 5.8 scripts
  6. The Gimp and ImageMagick image manipulation programs
  7. vips/nip2 enables manipulation with images of almost arbitrary size
  8. Linux Fedora operating system (PC)

1.1.3  How to use the atlas

Click through the introductory pages to the table of contents. Clicking on any chapter or subchapter will bring you to the text. Here you will find links to images; buttons on each image enable list of sings, picture details etc. (see bellow).

Screenshot while running this atlas:

In the background there is the window with the atlas itself. The main picture window (with arrows activated) is in the foreground, right. To the upper left there is a small window showing the detail (the detail is driven by mouse clicking in any site of the picture in the main window, see bellow). To the lower left there is a window with the list of signs; each sign can activate corresponding arrows in the main picture window.


Test: this image itself, window with arrows is enabled:
Atlas - screenshot, (1965)  Navigating through the text pages

Each page is provided with a row of buttons at top and bottom, allowing transfer to the previous and next chapter, back to the table of contents and to the index.

The logo Pi will keep its position when scrolling through the pages. Clicking this logo will bring you to the table of contents.

Clicking on a image link will open a window with one row of buttons, under which there will show the corresponding picture. The picture will be 900×900 pixels; its size will be adjusted when using low resolution monitor (under 1100 px vertically).  Controlling the pictures

You can have any numer of picture windows open at the same time. Each window is provided with a row of buttons:

  1.   opens or closes the window with the list of signs
  2.   opens the magnifying window
  3.   closes the magnifying window
  4.   closes the window with pictures
  5.   focusing up
  6.   focusing down
  7.   enlarging the basic picture, which can be dragged

Opens or closes the window with the list of signs. The list of signs is opened in a separate window. The text is generated from the database of signs and sometimes additional notes are added. When moving the mouse over the text of a sign description the background of the text changes to bright green and the arrow (or other signs) appear in the picture. After moving the mouse off the arrows disappear. After clicking on the sign description the background turns dark green and the arrows are fixed until another click.


Picture for testing the arrows:
Arrows verification, (522)

Opens the magnifying window. The small window with high resolution picture will open. The picture will scroll according to the user clicking in the picture with the basic picture, showing the detail. Note: Some pictures may not have the high resolution button available. That means such picture is available in low resolution only (fluorescence etc.)

Closes the magnifying window. Always use this button to close the high resolution window!

Focuses up in pictures available in several focusing planes.

Focuses down in pictures available in several focusing planes.

Closes the basic window (and associated windows with signs or high resolution as well). Always use this button to close the window!

Enlarges the basic picture by a factor of (approx) 2.5 (no image degradation will occur, but rather new details will appear). The image can be dragged by a mouse (click and hold the left button). The same button will decrease the size of the picture back. This button is available in those pictures, where there is large difference in size of the image in the basic and high resolution window. The arrows will deactivate the zoom and vice versa (the arrows work with the basic picture in normal size only). The high resolution window is available and functioning in zoomed-in pictures as well.

Not all the buttons are available in each picture!  Logos and labels

After opening the basic picture the logo is shown. In contributed pictures the label with the name and institution of the contributor is shown as well. The logo and label disappear after a while, so that the quality of the picture is not affected.

The logo, shown in upper left of each text page of the atlas is a place, where a tiny iconized preview of each picture is shown as a response to putting the mouse over the picture name. Clicking the mouse on the logo will get you back to the page with contents.

1.1.4  What will you need to use the atlas

Browsers Microsoft Internet Explorer, versions 4 or higher are required. Recently Konqueror works as well. Best results gives Mozilla/Firefox, version 2 and higher and MSIE 6 or higher. You must have JavaScript support enabled (and pictures downloading as well, naturally). Moreover, opening new windows must not be forbidden (Mozilla allows this). Java or cookies are not required. The JavaScript activation and browser version are checked at start and appropriate error message is given.

Mozilla allows to block opening new windows. This feature must be disabled (= opening new windows must be alowed), otherwise the atlas will not work.

Mozilla allows to block the Change Images feature. This feature must be disabled (= image changing must be alowed), otherwise the focusable images and automatic iconic preview will not work.

We suggest using the new versions of both browsers (MSIE over 6, Mozilla/Firefox over 2.0) or Konqueror (version from 3.5.9). For other browsers the atlas is not tested.

The stability of the Netscape is lower in UNIX X-Window environment (PC Linux, SGI workstation) than under Windows 95, 98, NT, XP or Vista. MacIntosh was not tested.

We suggest a monitor resolution 1024×748 pixels at least, color depth 24 or 32 bits (True Colors), monitor size at least 17". Monitor in resolution 1600×1200 pixels or more, 21", is the best choice.

The monitor will adjust the size of the windows to the lower resolution, bur the quality is worse and orientation is complicated if multiple windows are open.

The connection speed over 1 Mbit/s is necessary for comfortable use of the atlas. The mean size of a picture is about 1 MB, about 2 MB is the high resolution picture (sometimes more, up to 12 MB), the z-stack of images can be even larger.

If using connection with lower capacity avoid opening high resolution windows. Do not forget closing the unused windows with pictures, they eat up a lot of memory.

When opening the high resolution window the whole picture must be downloaded to your computer, not just the part scrolled into view!

1.1.5  Bugs, problems

Problems which could not be avoided:  Netscape
  1. Mozilla browser allows to block the change images feature, which is necessary for focusable pictures and for automatic iconic preview of all the pictures. In case you are using Mozilla and when moving the mouse over the name of a picture the Pi logo will not change, this feature is probably disabled. Similarly buttons will not react on mouse actions. (See Edit->Preferences->Advanced->Scripts&Windows)
  2. Animation of buttons sometimes does not work (version 4.5-7)
  3. Not very stable in UNIX (version 4.5-7)  Microsoft Internet Explorer
  1. Not available for UNIX platforms
  2. Sometimes the cursor does not change when over the links in the level of the logo (text part of the atlas). Probably the bug in Czech localization of some versions of the MSIE. Scroll the text down a little bit.
  3. Right mouse clicking raises sometimes an error (not harmful, just click to continue)
  4. Introductory page not rendered correctly (absolute positioning does not work properly), seems to be specific for Czech localization.

1.1.6  Some other Internet resources concerning dermatopathology and pathology

Meta pages, listing various resources
Martindale's Health Science Guide
PathMax, the WWW metaindex of sites pertinent to pathology education

Advanced dermatopathology, quiz-like, many cases:
DOIT: image collections, clinical information, quizzes and many other
Dermatopathology by Weems
Dermpedia: large collection of images and case studies

DermQuest: Image library, access to some publications

Clinical and histological pictures
Atlas of Dermatology
Dermatologic Image Database
Dermatology Image Bank

Clinical information and pictures
Dermatology Online Atlas (DOIA)
Pediatric Dermatology Online Atlas (PeDOIA)
Atlas Tunisien De Dermatologie Online
Dermatlas: Dermatology Image Atlas

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If you have problems running this atlas (eg. the windows with images do not open), you might have been referenced directly inside the atlas from some other web site. Thus you might have skipped some entry detection routines. Please try entering through the main web page of this atlas at: