Objectives:

From the lecture:

1. Understand the processes of preparing and viewing tissues by light and electron microscopy.



2. Understand the physical bases for the appearance of tissues in the light and electron microscopes (e.g. What is basophilia and what causes structures to be basophilic? What creates the contrasting light and dark regions in an electron micrograph?)

From the lab session:

3. Become familiar with the various ways to access and view images in the Michigan virtual slide collection

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

STEP 1: Plug in your computer (most laptops run faster when plugged in).

STEP 2: Disable your wireless connection.

• If you are unsure how to do this, ask for help from the LRC staff (or one of your colleagues).

STEP 3 (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!

Note that if you are using Internet Explorer, you can RUN the HistoDriveMap file directly from the website and it is perfectly safe to do so. If you want to have this option in Firefox, you should install the Open Download Add-on (click here to go to the Open Download Add-on site).

STEP 4 (Windows Only): Confirm and optimize installation of ImageScope v9.

• Launch ImageScope from Start->Programs->ScanScope->ImageScope. The upper left-hand corner of the window should say "Aperio ImageScope v.9.1.19.1569"



• If you haven't installed the latest version of ImageScope v9, click here to download the ImageScope installer (save it to your desktop). After downloading, double-click on the file (ImageScope_v9_1_19_1569_Installer.exe) to launch the installation program.



• 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, you MAY need to make some adjustments 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) if it is checked, but leave the "Progressive Rendering" option checked.

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
     

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_40X.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 IV. Load testing

This part of the session requires COORDINATED activity. DO NOT click on any of the links until instructed to do so.

Step 1. All users (Mac AND Windows):

A. Click on this [Mac] link to open a virtual slide.

-Once the slide is open, please try moving around and zooming in on the image.

 

Step 2 (Windows only). Opening several files simultaneously.

A. Click on this [WinLab] link to open 5 slides from the local file server.

-Take a moment to try moving around and zooming in each image (use the filmstrip to switch between images)

B. Click on this [WinLab] link to open 5 more slides from the local file server.

-This should add 5 more images to your filmstrip; again, try moving around and zooming in each image.

C. Click on this [WinHome] link to open 2 new slides from the web servers.

-This will close the previous images and open 2 new slides from our WEB SERVERS for you to try out.

D. Click on this [WinHome] link to open 5 slides from the web servers.

-This will open an additional 5 slides from our web servers for you to try out.

 

Part IV. 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 may be opened by clicking 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. Or you can delete the annotation by clicking on the "X" in the annotation window (see example).



5. Corresponding text can be entered 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 --BE SURE to 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 (see example) and select the file that you just saved; you should see the annotations that you generated in steps 4 through 6 above.
   
   
   
10. One thing to note is that ANY annotation file can be imported and overlaid on ANY slide --this is why it is important to include the slide number the annotation filename, so you'll know which file to import for a given slide. To illustrate this point, try opening slide #176 using this [WinLab] link or this [WinHome] link and then import the slide #29 annotation file that you generated in the steps above. Notice that the annotations are overlaid on the slide, but probably in a manner that doesn't make sense.

Part V: Using WebViewer ("Mac" links) to Create "Bookmarks" to Regions of Interest

Unfortunately, there is currently not a way to annotate slides viewed with the WebViewer (i.e. "Mac" links). However, you can at least create "Bookmarks" to regions of interest on a slide that you can use to quickly open a slide and take you back to a particular region.

1. Open Slide #126 using this [Mac] link.
   
   
2. Find a region of interest.
   
   
3. To bookmark that region, click on the "checkmark" icon in the toolbar (see example).
   
   
4. A new window (see example) will appear giving you a link that can be used as a "bookmark" for WebViewer (i.e. a "Mac" link) and a similar link to open that same view in ImageScope. Clicking on the WebViewer link will take you to that specific view and you can then use the "Add Bookmark" tool on your browser to add it to your bookmarks.

A less convoluted way is to just RIGHT-click on the URL and you'll be given the option to bookmark the link directly from that page. Alternatively, you could type some descriptive text in a Word document and then create a hyperlink to that URL:

1. use the mouse to highlight and copy the WebViewer link (or just RIGHT-click on the link and select "Copy Link Location")
2. launch Microsoft Word and type some short descriptive blurb of the region
3. select the text in the Word document, then either:
   1. RIGHT-click on the selected text, choose "Hyperlink" from the list of options, and PASTE the URL into the address field (see example), OR...
   2. Go to the "Insert" menu, choose the "Hyperlink" option, then PASTE the URL into the address field (see example).

Part VI: Wrap-up

When you are finished in the lab:

A. (Windows only) Disconnect your mapped network drive

• This will help your computer boot faster when you are off the campus network.
• Look in My Computer for the mapped drive "Images on 'ONStor EverON(172.20.57.42)’(Z:)".
• Right Click on the mapped drive and select Disconnect.

B. (ALL users) Shut down, disconnect network cable, etc.

If you experience any technical problems, see one of the LRC staff or E-mail: lrc_help@umich.edu