Digital Microscopy Topics

Part I. Set up to access the virtual slides on campus

STEP 1: Connect via network cable and disable your wireless connection

• In general, a wired connection is almost always faster than wireless.
• If you are connecting via a network cable, you should DISABLE your wireless antennae (otherwise, your computer may attempt to connect the wireless network resulting in slower performance).

STEP 2 (Windows users only): Create a mapped drive to the virtual slide file server for "on-campus" access if you have not already done so.

• Click here to download the "HistoDriveMap" batch file (click on the link and save the file to your desktop). Double click on the file on your desktop to create the mapped drive. YOU SHOULD RUN THE "HistoDriveMap" FILE EACH TIME YOU RESTART YOUR COMPUTER AND CONNECT TO THE CAMPUS NETWORK!

STEP 3 (Windows only): Confirm drive mapping.

• If you look in "My Computer," you should see an additional drive called "Images on 'ONStor EverON(172.20.57.42)’(Z:)"

STEP 4 (Windows Only): Install ImageScope v8.

• If you haven't installed ImageScope v8, click here to download the ImageScope installer (save it to your desktop). After downloading, double-click on the file (ImageScopeInstaller.exe) which should launch and install ImageScope v8 automatically.


• If you have a previous version of ImageScope installed, the installer may ask if you want to Modify, Repair, or Remove the previous version. Select "Repair," (see example) then click "Next."

To optimize performance of ImageScope, there are some adjustments to make to the default settings:

• Go to the "Tools" menu, then "Options". In the Options window, click on the "Performance" tab and UNCHECK the "Prefetching" option (see example).

PART II. The Basics

A. Accessing the Digital Slides

There are currently 3 different ways to access the slides, so you will see 3 different links for each digital slide in the online lab modules:

1. [WinLab]: use this link when ON CAMPUS (requires a Windows machine with ImageScope installed AND a mapped network drive to the high-speed file server)



2. [WinHome]: use this link when OFF CAMPUS using a Windows machine with ImageScope



3. [Mac]: this link will work on ANY machine ON or OFF CAMPUS, but it is really intended for those who are unable to run ImageScope (i.e. non-Intel Macs)

When in the lab, using the [WinLab] links is PREFERRED as this will ALWAYS deliver the images at the highest speed.

To help you remember, you will find the following table at the beginning of each lab module:

B. Viewing slides on the web server using "[Mac]" links.

• Click on this [Mac] link here to open slide 29 from the digital slide collection. A new window should open containing the digital slide. You can drag and re-size this window to your liking. Note that pop-up blockers (such as Google) may require you to allow pop-ups from this site. Take some time to use some of the basic features of the viewer such as panning and zooming.

C. Viewing slides on the local file server using "[WinLab]" links.

• Click on this [WinLab] link to open slide #29 in ImageScope. This link points to a small file (a .sis file) that should launch ImageScope and open the slide. If you are doing this for the first time, Internet Explorer may ask "Do you want to open or save this file?" You should uncheck the box that says, "Always ask before opening this type of file," then select Open.

• Once slide 29 has been opened in Imagescope, you may drag and re-size the window to your liking. Take some time to use some of the basic features of the viewer such as:
  
  
  1. panning and zooming
  2. filmstrip view (under the "View" menu)
  3. thumbnail view
  4. magnifier view
     

If you are using ImageScope for the first time, the default view will be something like what is shown below. The viewing options are explained below and may be changed by checking/unchecking these options in the “View” menu.

1. Filmstrip:

• If you have multiple images open, you can easily move between images by simply clicking on the thumbnails in the filmstrip

2. Magnification slider:

•You may click on a button to jump to a particular objective power; note that the numbers (2x, 4x, etc.) correspond to the objective lenses of a light microscope and NOT the final magnification.

• The magnification also may be changed by moving the slider bar using the mouse

• The mouse scroll wheel will also control the magnification

3. Image thumbnail:

• This provides you with an orientation as to which region of the slide you are viewing. Zoom in a particular region of interest, and you’ll see a red box on the image thumbnail outlining the region you are viewing.

4. Image:

• As you mouse over the image, you’ll see that the pointer is a hand that allows you to grab the image and move it in any direction. Clicking on the scroll wheel activates the “pan” mode that allows you to move across the image by simply moving the mouse (the panning speed corresponds to the distance the mouse is moved).

5. Magnifier:

• This provides 2x magnification of a region of interest. The region of interest may be selected by simply moving the mouse to that region or you can grab the magnifier window and move it around the slide (as you might use a magnifying glass)

6. Status bar:

• The status bar provides information regarding the overall size of the image (in this case 145,545 x 92,372 pixels), the raw file size (37.6 GB), and the compressed file size (1.5 GB). The second column in the status bar indicates the coordinates of pixel located in the upper left corner of the image and the total size of the region being viewed. The third column indicates the actual coordinates of each pixel indicated by the pointer as the mouse is moved over the image.

D. Viewing slides on the web server using "[WinHome]" links.

• Click on this [WinHome] link to open slide #176 in ImageScope. "[WinHome]" links are to be used when viewing this site from OFF CAMPUS or if you have any difficulty using the [WinLab] links. (The [WinHome] links will work on campus, but the performance will likely be slower.)



• Notice that your filmstrip now contains slide #29 (029-1_HISTO_40X.svs) and slide #176 (176_HISTO_20X.svs). You may switch between the two by clicking on the thumbnails in the filmstrip. You can also "tile" the two slides for side-by-side comparisons (under the "Window" menu).
  

Part III. Using Annotations in ImageScope

One of the main advantages of viewing the virtual slides in ImageScope is the ability to annotate the images in a "layer" that you can then save to your own computer (the original image on the server is not altered in any way).

1. To begin making annotations, go to a slide of interest, in this case we will use slide #29, which you should have open already. If not, click on this [WinLab] link (if your computer cannot connect to the file server due to drive-mapping issues, you may use this [WinHome] link instead).



2. Begin by opening the "Annotations" window (under the "View" menu or by pressing Crtl+N)



3. Go to an area of interest, then select an annotation tool from the toolbar (see example)



4. Once an annotation tool is selected, the pointer will change to a small "pen" icon. Click and drag to draw the the annotation on the image; finish by releasing the mouse button. If you do not like to placement of the annotation graphic, it may be moved by pressing the Ctrl key and then clicking on the graphic with the mouse.



5. Entering text in the "Annotations" window to go along with the annotation graphic:
   • in the "Text" column: text entered here will also be displayed on the image
   • in the "Description" column: text here is NOT displayed on the screen



6. After generating additional annotations, you may quickly move from one annotated region to another by clicking on rows within the "Annotations" window. You can also "hide" the annotations by clicking on the "Show/Hide Layers" icon (it looks like an eye).



7. Save the annotation file by Exporting it to your computer's hard drive. Be sure to use the "Export Annotations To File" icon (see example) and name the file accordingly (e.g. include the slide number in the filename).



8. Now, CLOSE slide #29. You should get an alert box saying "One or more annotation layers have been modified... Do you want to save the changes?" Select "No".



9. Now, we'll see how to use the annotation files once they've been saved to your computer. Re-open slide #29 using this [WinLab] link or this [WinHome] link. Click on the "Import Annotations To File" button in the "Annotations" window and select the file that you just saved; you should see the annotations that you generated in steps 4 through 6 above.