The Virtual Slide display

The display is separated into two regions:

  • The Slide (or Main) window where the tissue can be viewed at one of several magnifications;
  • The Macro view area, which shows a thumbnail of the entire slide lens;

Navigation is done entirely by means of your mouse. Clicking in either the macro area or the slide area will center the slide area on the point you click. Dragging in either window will move the currently visible region. To zoom in and out, select the desired magnification from the drop-down list at the top of the macro area, or use the magnifying glass icons to zoom in and out.

Adding an Annotation

An Annotation is a remark, question, or note that appears in a bulleted format in the window below the Slide window. The Annotation is saved at the Virtual Slice host along with the coordinates of the location that it refers to, the labels you have added, and the magnification in effect at the time you entered it. Users will see all the comments in the Annotations area under the Slide window. The comments will be in plain text or HTML format. When a user clicks on an Annotation bullet the screen automatically pans and zooms to the region where the Annotation was made. The region will be displayed at the same magnification the Annotation was added and will display any labels that have been added.

You must have sufficient permission to add an annotation. Use the 'log on' button on the toolbar to log in. You will be shown the different groups that you have permission to view or edit.

To enter an annotation, view the slide as you normally would, then look for the Add Annotation hyperlink button at the bottom of the area. You will be transferred to a new page that contains the annotation tools.

Add an Annotation

First, Pan and zoom in the Slide window until you are looking at the relevant area of the material. When your Annotation is chosen, the Slide View will return to this view at this magnification.

Next, (optionally) use the Label tab in the Toolbox to draw any arrows or text that would help clarify your discussion of this field of view. These will be displayed when your comment is chosen.

Finally, enter your comment as text in the Add Annotation window. Users will see this in the Comment area under the Slide window. This can be plain text or HTML source. Click the Add this Annotation button beneath the Add Comment window when you are done.

Tip: Draw your labels near the center of the Slide window. Other users may have a smaller field of view on their web browser screens when they view the slide region that your comments pertain to. Any label components that are drawn near the edges of the Slide window are at risk of being outside the field of view for such users.

Labeling Tools

Using the toolbox one can place text and/or arrow overlays on the section, or to edit an existing label. You can create or edit a label at any time. If you add an Annotation, your labels will be stored for others to view when this section is selected for viewing.

There are several tools in the toolbox. The five buttons on the top are for placing text, arrow, text combined with arrow, a Monocle with text, or drawing a boundary contour. The three buttons below them are for placing markers triangle, closed circle, and cross. The two buttons on the right, red arrow and X, are used to edit label components. The red arrow works as a 'select' arrow, the X is used for deletion.

Any label you place will be visible throughout the specific magnification levels that you have selected. If a label is selected, a pull down menu called 'visible' will appear, which can be used to limit visibility of the label to the current magnification, or to the current magnification plus and minus one or two levels of magnification.

Adding and editing text**

Choose the T button to overlay text. First, enter the desired text in the text window below the toolbar. Next, in the Options controls below the toolbar choose a color that contrasts with the tissue. Styles and visibility range can also be edited here. Finally, click on the location in the Slide Window where you wish to place the text.

The available text options include:

  • Color - the color of the label
  • Size - the point size of the font used for text
  • Style - the font style
  • Visible - the levels of magnification at which the label will be visible.

To edit existing text, click on the red arrow selection tool and then, in the Slide Window, click near the center of the text you wish to modify. A white square 'handle' appears within that text. You can move the text with the mouse by dragging it by the handle. Other changes can be made to the text using the box below the toolbar, but only while the text is selected. To delete the text, click on the red X delete button after clicking on it with the selection tool. (Some browsers also support pressing the keyboard delete key.)

Adding and editing arrows**

Choose the arrow button on the toolbar to draw arrows. First, select a color for the arrow. Next, click the left mouse button where the tip of the arrow should be and hold the mouse button down. Now, drag the mouse to position the arrow’s tail. Should you then wish to draw another arrow, click where the head of the subsequent arrow should be and it will have, by default, the same length and orientation as the first arrow.

Other available arrow options include:

  • Color - the color of the label
  • Thickness - the arrow thickness
  • Visible - the levels of magnification at which the label will be visible.

To edit existing arrows, click on the red arrow (i.e., the selection tool). Then, click near the tip of the targeted arrow. Handles will appear which can be dragged. The handle at the tip of the arrow moves the location, the one at the tail alters the orientation and size of the arrow. You can also change any attributes of the arrows (e.g., color or thickness). To delete the arrow, click on the red X delete tool click on the red X delete button after clicking on it with the selection tool. As mentioned above, some browsers also support pressing the keyboard delete key.

Adding and editing arrows with text**

This option is drawn just like an arrow, but allows you add text that is linked to the arrow. The text is always positioned at the tail of the arrow and will stay with the arrow at the various magnifications without "floating away" at different zoom levels. (Try it!) To select Arrow with Text, click on the T/Arrow tool. Next, as before, enter text in the text window and choose your other options. Then click on the point in the Slide window where you want the tip of the arrow to be. (The text must be entered first) To position the arrow and orient it, click on the red arrow selection tool. Drag the arrow handles as described above. Note that you can delete an arrow and its linked text as a unit, but not the text by itself.

Other options for arrows and text include:

  • Color - the color of the label
  • Size - the point size of the font used for text
  • Style - the font style
  • Thickness - the arrow thickness
  • Visible - the levels of magnification at which the label will be visible.

Adding and editing Monocle With Text**

This feature allows one to highlight an area using a circle with attached text. Select the monocle with text tool, then select a color appropriate for the image. Enter text in the text window, set the other options, then click and drag on the image to draw a circle over the desired area. Click again to place the text. The text will have a line drawn automatically which connects it to the circle (the text may be inside or outside the circle. The size and position of the circle, as well as the position of the text, can be changed using the selection tool.

Other options for Monocle With Text include:

  • Size - the point size of the font used for text
  • Style - the font style
  • Thickness - the arrow thickness
  • Visible - the levels of magnification at which the label will be visible.

Adding and editing contours**

Click on the boundary contour tool, then select a color for the boundary. Left-click on the image to begin drawing a boundary. To draw a curved boundary hold down the left mouse button and use the cursor to draw a contour over the image. To draw a contour with straight sides left-click the initial point and release the button. Then move the cursor to the next spot and click a new point--a line will automatically be drawn between the first and second points. To add more line segments to the boundary, simply click additional points. Both types of contour can be left open (by selecting the "End" button in the options area) or can be closed (by selecting "Close").

Available options for contours include:

  • Color - the color of the contour line
  • Thickness - the point width of the contour
  • Line Style - the type of line (dotted, dashed, solid)
  • Visible - the levels of magnification at which the label will be visible
  • Visible Mag - the levels of magnification at which the contour will be visible.
  • Description - text entered here will appear in a small text box when a user's cursor is over the contour
  • Link - entering a web address in this line links the contour to a web site--when a user clicks on the contour, the website is opened in a new window
  • Delete Last Point - deletes the last point added to a contour

To edit an existing contour, click on the contour with the selection arrow. All of the points in the contour should light up as small, white squares. Click on a square and drag it to move the point (the lines will move with the points).

If you have purchased the Atlasing System, the contour system has a much wider range of capabilities. Within the shared boundary system, you are able to fill in the enclosed region with color and alter the transparency of that color, so as to be able to see the slide. In addition, you may group multiple contours together and alter the properties of all grouped contours at one time. With respect to the contour lines, you can change the line styles, colors, etc of the different contours at the same time.

Adding and editing triangle marker**

Choose the triangle button to overlay this marker. First, in the Options controls below the toolbar choose a color that contrasts with the tissue. Size and visibility range can also be edited here. Finally, click on the location in the Slide Window where you wish to place the marker.

The available triangle marker options include:

  • Color - the color of the triangle
  • Size - the pixel size of the triangle (from center to a vertex point)
  • Visible - the levels of magnification at which the label will be visible.

To edit existing triangle, click on the red arrow selection tool and then, in the Slide Window, click near the center of the triangle you wish to modify. A white square 'handle' appears within that triangle. You can move the triangle with the mouse by dragging it by the handle. If you drag the mouse on the white square, positioned at the vertex of the triangle, the triangle will automatically resize. Other changes can be made to the triangle using the box below the toolbar, but only while the triangle is selected. To delete the triangle, click on the red X delete button after clicking on it with the selection tool. (Some browsers also support pressing the keyboard delete key.)

Adding and editing closed circle marker**

Choose the closed circle button to overlay this marker. First, in the Options controls below the toolbar choose a color that contrasts with the tissue. Size and visibility range can also be edited here. Finally, click on the location in the Slide Window where you wish to place the marker.

The available closed circle marker options include:

  • Color - the color of the closed circle
  • Size - the pixel size of the triangle (from center to a vertex point)
  • Visible - the levels of magnification at which the label will be visible.

To edit existing closed circle, click on the red arrow selection tool and then, in the Slide Window, click near the center of the closed circle you wish to modify. A white square 'handle' appears within that closed circle. You can move the closed circle with the mouse by dragging it by the handle. If you drag the mouse on the white square, positioned at the edge of the closed circle, the closed circle will automatically resize. Other changes can be made to the closed circle using the box below the toolbar, but only while the closed circle is selected. To delete the closed circle, click on the red X delete button after clicking on it with the selection tool. (Some browsers also support pressing the keyboard delete key.)

Adding and editing plus sign marker**

Choose the plus sign button to overlay this marker. First, in the Options controls below the toolbar choose a color that contrasts with the tissue. Size and visibility range can also be edited here. Finally, click on the location in the Slide Window where you wish to place the marker.

The available plus sign marker options include:

  • Color - the color of the plus sign
  • Size - the pixel size of the triangle (from center to a vertex point)
  • Visible - the levels of magnification at which the label will be visible.

To edit existing plus sign, click on the red arrow selection tool and then, in the Slide Window, click near the center of the plus sign you wish to modify. A white square 'handle' appears within that plus sign. You can move the plus sign with the mouse by dragging it by the handle. If you drag the mouse on the white square, positioned at the vertex of the plus sign, the plus sign will automatically resize. Other changes can be made to the plus sign using the box below the toolbar, but only while the plus sign is selected. To delete the plus sign, click on the red X delete button after clicking on it with the selection tool. (Some browsers also support pressing the keyboard delete key.)

Adding and editing segments with text**

Note: This option only works if you have previously drawn a contour on form and have purchased the Atlasing system. This option allows you to label different portions of your contours with text. The text is always initially positioned between the two boundary lines, but can be moved. To select the Segment Text, click on the T/Boundary tool. Next, as before, enter text in the text window and choose your other options. Then click on the first boundary point in the Slide window. You will see a boundary marker being placed perpendicular to your line. Then click on the second boundary location and you will see the second boundary marker place perpendicular to your line. In addition, the text that you have entered will be centered between the two boundary markers. To position the text or the boundary markers, click on the red arrow selection tool. Drag the text or boundary handles as described above.

Other options for arrows and text include:

  • Text - the text shown between the contour lines
  • Color - the color of the label
  • Size - the point size of the font used for text
  • Style - the font style
  • Visible - the levels of magnification at which the label will be visible.
**In order to save the contours, arrows, or text one must completely add an Annotation.

Virtual Slide FAQ

Q1. What happens when I select a section to work with?

A1. After you log into the Virtual Slide host and select a section to examine, the viewer loads. The viewer is a relatively large Java Applet (160K bytes) so this can take 30 - 45 seconds on a slow Internet connection. As soon as the viewer starts, it downloads the macro image. The slide window then immediately begins downloading square tiles at the current magnification until the current field of view is entirely visible. As you pan and zoom, more tiles will be requested and filled in. Up to 8 Megabytes worth of tiles are in memory at any one time.

Q2. How long does a download take?

A2. Download time depends upon the speed of your link to an Internet provider and to the size of the image you choose to view. Each tile is 13K bytes, and a field of view typically contains 8 tiles or about 100K bytes. Dial-up connections can be as slow as 4K bytes per second, so a field of view may take up to 25 seconds. For high-speed Internet links, download time should be a matter of a few seconds.

The internal speed of your computer has little effect on download time.

Q3. What happens during panning and zooming?

A3. Because of the image size of the slice that is stored at the Virtual Slide host, it is impractical to download all of it to your site at once. Only those parts that you need to work with are downloaded at the start. When you choose to view a different part of the slice, your computer transmits a signal to the Virtual Slide host requesting more image data. The image data is then downloaded. Sometimes, because of the image storage capabilities of your computer, image data already stored in your computer is erased in order to make room for the new data. (Note: you will notice this in the informational window overlaying the upper left part of the image. It tells you the download status of the field of view that you are viewing.) Generally, the downloaded image data pertains to the field of view you have selected and the fields that are adjacent to it.

Q4. What happens when a Virtual Slide session is terminated?

A4. All image information is erased from your computer except that which is contained in the screen you are viewing. Any overlay information that you have created is transmitted backed to the Virtual Slide host and incorporated with the slice you were working with. It is not made a part of the image file itself but is contained within an ancillary file linked to the image. It will be available the next time you use Virtual Slide to access that image.



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