Overlays

The overlays transform provides a means for creating graphical overlays--such as lines, ovals, boxes and text--atop another data object. Overlay annotations are useful for many reasons: dividing a complex image into scientifically relevant sections, measuring numerical characteristics, and demonstrating biological phenomena for instructional purposes, for example.

Creating a set of overlays

To create a set of overlays, first import your dataset as described in the Importing a dataset from disk topic. Select your dataset from the list, then click the "Add >" button and choose "Overlays" from the popup menu.

Choose a name for the overlays, and VisBio will create another data object, a child of your original dataset, that represents the overlays. To access the tools for drawing overlays, select the overlays and click the "Edit" button. A window similar to this one will appear:

Parameters for overlays

To begin drawing overlays, you must first display them in 2D atop the parent dataset. First, add your dataset to a 2D display as described in the Displaying a data object topic. Then add the overlays to the same 2D display (not a new one). Doing so will overlay them atop your image.

[Author's note: On some systems (in particular, if VisBio is using Java2D because Java3D is not installed), the rendering order of the dataset and the overlays may need to be reversed. If you see nothing when drawing overlays, select the overlays from the display window's list of linked data objects and click the "Up" button to move them up in the rendering order.]

Drawing new overlays

To draw an overlay, choose the appropriate tool from the "Tools" section of the overlay controls. The tools shown above (from left to right) are: pointer, line, freeform, marker, text, oval, box, arrow, and polyline. In many ways, they behave like similar tools available in many image editing programs. To use a tool, click the associated tool button.

Altering existing overlays

You can use the overlays controls to alter the characteristics of selected overlays. First use the pointer tool to select the overlays you wish to change, or select them from the overlay list on the left side of the "Overlays" section of controls. Note that the overlay list only shows overlays for the current dimensional position.

To remove an overlay, click the "Remove" button or press the Delete key.

To copy overlays to the clipboard, first select them, then click the "Copy" button or press the Ctrl+C key combination.

To paste overlays from the clipboard onto the current image plane, click the "Paste" button or press the Ctrl+V key combination.

To change an overlay's position, click and drag it using the pointer tool, or type in new values directly for the (X1, Y1) or (X2, Y2) coordinate values.

To change the text shown for a Text overlay, click the text object to select it, then type new text, or type new text directly into the "Text" box.

To change the color of the selected overlays, click the button labeled "Color" to bring up a dialog box for choosing a new color.

Some overlays--ovals, boxes and arrows--can be filled in (solid) or outlined (hollow). To toggle which for the selected overlays, use the "Filled" checkbox.

Each overlay allows you to store one line of miscellaneous notes. To make a note for the selected overlays, type your note into the "Notes" text box.

Grouping overlays

Each overlay has an associated group. This feature is useful if one collection of overlays tracks a particular phenomenon, while another collection of overlays tracks another phenomenon. In this case, each collection can be assigned to a different group to differentiate between the collections.

To choose the group to which the selected overlays belong, choose a group from the "Group" dropdown box. New groups can be created by clicking the "New..." button next to the "Group" box.

Distributing overlays

VisBio's distribution feature allows for linear distribution of an overlay across many consecutive image planes. By identifying starting and ending overlays, you can instruct the software to create a series of intermediate overlays between the starting and ending image planes.

First, decide on a series of image planes across which you wish to distribute an overlay. For example, you could decide you want an oval overlay on slice #5, from timepoints #3 through #57.

Navigate to the first image plane and draw the overlay. In our example, create the oval at slice #5, timepoint #3.

Copy the overlay to the clipboard by clicking the "Copy" button (or by pressing the Ctrl+C key combination).

Navigate to the last image plane and draw the same type of overlay (or paste the copied overlay onto the exact same coordinates using the "Paste" button, or by pressing the Ctrl+V key combination). In our example, create or paste the oval at slice #5, timepoint #57.

Finally, click the "Distribute" button. To see what VisBio has done, navigate through the intermediate frames. In our example, move the Time slider between #3 and #57 to see how VisBio has distributed oval overlays.

Changing the font

Each set of overlays uses a particular font to display text overlays. The font being used is shown in the "Font" text box. To change it, click the nearby "Change..." button. A dialog box will pop up allowing you to select a new font. Please note that this setting affects all text overlays in the set, not just the selected ones.

Saving your work

You can save your overlays to a tab-delineated text file on disk (readable by spreadsheet applications for further analysis). Click the "Save overlays..." button to do so, and a file browser will appear. The tabs on the right side of the file browser allow you select which overlay statistics you would like saved in the spreadsheet file. Note: the statistics which appear in these files are for your convenience only--VisBio will recalculate all statistics, saved or not, when the overlays are loaded.

You can restore saved overlays by using the "Load overlays..." button and choosing a text file saved earlier. Please note that loading an overlay set will clear out any current overlays, overwriting them with those saved in the text file.

You can export your overlays to .xls spreadsheet format using the "Export Overlays..." button. As when saving overlays, you may select the statistics you wish to save in the file. VisBio uses the Apache POI HSSF library to write .xls spreadsheets.

See also: