User Guide

User Guide

Running

To run the application you need to install a Java Runtime Environment 8.

The application does not require installation, just extract the downloaded .7z file with a zip utility (such as 7-zip or FileArchiver) and double click on a VirtualSlideViewer.jar file.
Alternatively, the application can be started from a command line by entering the command:
java -jar path/to/a/VirtualSlideViewer.jar

After the application has been started you should see the following window:

Virtual slide loading

As is written on the welcome screen to load a virtual slide click on the „File” menu entry in the top left corner of the window and select „Open...”. After that you should see a window asking you for a path to a virtual slide. Select a virtual slide you want to load and click the „Open” button.

After you confirm your choice you should see a window telling you about the slide loading:

If you want to cancel the loading just click the “Cancel” button.

After a few seconds the window should disappear and the main window should switch to a view similar to:

After the slide has been loaded you should choose the image you want to view. To do it you need to choose a series in a series panel located at the bottom right corner of the application's window:

There you can see the thumbnails of the series. To display an image just double click on its thumbnail or select it with a single click and press the “Enter” key. An alternative is to click the right mouse button while pointing at the thumbnail and select the “Show” entry from a menu which has just popped up.

The renaming and removal of a series

From the context menu of series panel you can also rename or remove the series. Just choose the “Rename” or “Remove” entry or click the action's shortcut key, respectively, “F2” and “Delete” when the menu is not visible.

After doing some of the above actions, a status bar will appear in the bottom of the window telling you what action has been done.

If you want, you can undo the action by pressing the “CTRL+Z” key combination or by clicking the “Undo” entry in the “Edit” menu:

As you can see in the above screen you can execute the action again by pressing the “CTRL+Y” key combination or by clicking the “Redo” entry.

Zooming

After you choose the series in series panel, the main navigation panel will display the entire image. To zoom the image point the mouse cursor at the point you want to zoom at and rotate the mouse wheel in the forward direction until you get the desired zoom level. To zoom out, do the same but rotate the wheel in the opposite direction.

By default after every wheel rotation the image is increased by 10% of its current size. The zoom sensitivity can be changed in the preferences window:

To open this window select a “Preferences” entry from the “Edit” menu.

The sensitivity of zoom can be changed by modifying the “Zoom increment” value. Increasing the value with make the zoom increase the image size faster, for example if you enter the value 2, the image will double its size after every rotation of the mouse wheel.

In the preferences window you can also see a mysterious option called “Resolution transition threshold”. This option controls the sharpness of the image after a zoom. The lesser the value the better is the quality of the zoom. But beware that modifying this value can cause a big performance impact.

Besides of using the mouse wheel you can also change the zoom level with the usage of a slider located just above the series panel:

The zoom level can be changed either by dragging the handle of the slider or by entering desired zoom percentage into the text field.

Navigation

To navigate to a different part of the image you should press the left mouse button and move the mouse.

Above the zoom slider there is a preview panel:

This panel shows the location of visible part of the image with a green rectangle.

Besides showing the current location, the panel also allows you to quickly navigate to a arbitrary part of the image. You only need to click with left mouse button on the desired point on a preview and it will be centered on the main panel.

Channel switching

If the chosen series contains more than one channel, Z plane or time point, the application will show sliders at the top of the main panel which allows you to change the currently visible plane of the image.

To change the desired plane of the image you should drag the handle of the slider until the desired image is displayed. Alternatively, to quickly change the plane, for example to the same image acquired under different conditions you can use the shortcut keys: - Q and E, respectively, decrements and increments the index of displayed channel, - A and D, respectively, decrements and increments the index of displayed Z plane, - Z and C, respectively, decrements and increments the index of displayed time point

Panel customization

Every panel of the main window can be resized. To do it point the mouse cursor at the column separating the panels and drag it while holding the left mouse button. The panels can also be maximized thus hiding the other panels by clicking one of the arrows located at the top of the column:

Saving

After you have done some changes to the virtual slide, such as renamed or removed some of its series or you want to convert the image from its original format to a OME-TIFF you can use the save function.

To save the image select the “Save” or “Save as...” entry from a “File” menu:

The “Save” option causes the changes to be saved in the original file if the saving to its format is supported by the application. Currently, the application supports saving only to a OME-TIFF format. If the format is unsupported, the function will behave the same as “Save as...” option. The “Save” option is inactive until the slide is modified.

The “Save as...” option allows you to save the virtual slide to a different file and / or different file format. After you choose this option a window asking for a destination path will appear.

After the saving has been started, you will see a window showing you the progress of the save operation:

Due to huge sizes of virtual slides, the save operation is very long. Depending on the performance of your computer and the size of slide the operation can last from a few minutes to even a few hours.

After the virtual slide has been successfully saved, the progress window will close and the slide will automatically be reloaded.