E-mail of the main author of this atlas:
jfeit@ics.muni.cz
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.
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 (Merzhäuser) 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×oil.im./1.40 and CFI VC 100×oil.im./1.40 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.
Clicking on the link to a picture activates the virtual microscope interface. It may open into a new window or a new tab, depending on the setup of user's browser.
Virtual microscope enables manipulation with the image. The interface is the same for all the images, but actual options depend on the image type. For example users can switch image planes, but only in those images, which were taken in more than one focusing plane.
Users can modify the interface to some extent (e.g. the language).
There are three levels of access to the virtual microscope: for users, teachers and authors.
This text describes the possibilites users have when accessing the images.
There are 3 scrollbars at the upper left part of each image:
Zvětšení: posuvníkem nebo kolečkem myši lze obraz zvětšovat a zmenšovat podle potřeby. Při zvětšování kolečkem je centrum zvětšovaného obrazu dané aktuální polohou kurzoru. Malé obrazy (typicky snímky z CT nebo MR) lze zvětšovat i nad 100% velikosti původního obrazu.
Obrazová kvalita: při pomalém spojení lze snížit kvalitu obrazu a tím i velikost dílků, posílaných serverem. Naopak pokud plánujeme sejmutí části obrazovky s virtuálním mikroskopem, lze kvalitu zvýšit. Pro běžné účely doporučujeme nechat nastavenou hodnotu.
Rovina: posuvník nebo kolečko myši při současném stisku klávesy CTRL umožňuje posun mezi rovinami. V případě histologických obrazů dojde k proostřování, v případě snímků z CT, MR aj. tak lze procházet mezi nasnímanými rovinami. Tato možnost není k dispozici u obrazů snímaných jen v jedné rovině.
Obrazem lze pohybovat tažením myší. Lze takto pohybovat jak obrazem samotným, tak obdélníkem, zachycujícím viditelnou část obrazu v náhledovém okně vpravo nahoře.
Pokud (typicky při zvětšování) je možné zobrazit jen část obrazu, otevře se v pravé horní části obrazu náhledové okno. Modře ohraničená část obrazu odpovídá zobrazené části a lze jí tahem myší pohybovat stejně jako hlavním obrazem.
Náhledové okno je možné i manuálně otevřít a zavřít tlačítkem s černým trojúhelníkem.
V horní části obrazu jsou tři tlačítka. Prostřední tlačítko přizpůsobí velikost obrazu velikosti okna. Levé a pravé tlačítko (se šipkou) slouží k přechodu mezi historií poloh virtuálního mikroskopu (podobně jako tlačítka Vpřed a Vzad u webového prohlížeče).
U obrazů, které jsou anotovány, lze aktivovat šipky malým tlačítkem s černým trojúhelníkem v pravé části okna. Šipky se objeví, pokud se umístí myš nad některý ze seznamu znaků a spadá do aktuálně zobrazené části obrazu. Dále se objeví jako body v náhledovém okně.
Cvaknutím lze znak uzamknout (objeví se ikonka zámku) a šipky příslušného znaku zůstanou aktivní i pokud se posune myš mimo seznam znaků. Opakované cvaknutí znak odemkne.
Okno se šipkami lze obdobným způsobem zavřít.
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.
Pictures
Test: this image itself, window with arrows is enabled:
Atlas - screenshot, (1965)
You can have any numer of picture windows open at the same time. Each window is provided with a row of buttons:
opens or closes the window with the list of signs
opens the magnifying window
closes the magnifying window
closes the window with pictures
focusing up
focusing down
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.
Pictures
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!
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.
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!
Problems which could not be avoided:
change imagesfeature, 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)
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