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3<p>The overlays transform provides a means for creating graphical
4overlays--such as lines, ovals, boxes and text--atop another data object.
5Overlay annotations are useful for many reasons: dividing a complex image into
6scientifically relevant sections, measuring numerical characteristics, and
7demonstrating biological phenomena for instructional purposes, for example.
9<br><h3>Creating a set of overlays</h3>
11To create a set of overlays, first import your dataset as described in the
12<a href="import_data.html">Importing a dataset from disk</a> topic. Select your
13dataset from the list, then click the "Add &gt;" button and choose "Overlays"
14from the popup menu.
16<p>Choose a name for the overlays, and VisBio will create another data
17object, a child of your original dataset, that represents the overlays. To
18access the tools for drawing overlays, select the overlays and click the "Edit"
19button. A window similar to this one will appear:
21<p><img src="overlays.png" alt="Parameters for overlays">
23<p>To begin drawing overlays, you must first display them in 2D atop the parent
24dataset. First, add your dataset to a 2D display as described in the
25<a href="display_data.html">Displaying a data object</a> topic. Then add the
26overlays to the same 2D display (not a new one). Doing so will overlay them
27atop your image.
29<p><i>[Author's note: On some systems (in particular, if VisBio is using Java2D
30because Java3D is not installed), the rendering order of the dataset and the
31overlays may need to be reversed. If you see nothing when drawing overlays,
32select the overlays from the display window's list of linked data objects and
33click the "Up" button to move them up in the rendering order.]</i>
35<br><h3>Drawing new overlays</h3>
37To draw an overlay, choose the appropriate tool from the "Tools" section of the
38overlay controls. The tools shown above (from left to right) are: pointer,
39line, freeform, marker, text, oval, box, arrow, and polyline. In many ways,
40  they behave like similar tools available in many image editing programs.
43  <li>The <b>pointer tool</b> is for selecting existing overlays. Click an
44    overlay to select it. Use Shift+click to add the clicked overlay to the
45    selection. Use Ctrl+click to add or remove the clicked overlay to or from
46    the selection. Selected overlays have a yellow glow surrounding them.
47    Information about the selected overlays is shown in the "Statistics" area
48    at the bottom of the overlay controls.</li>
49  <li>The <b>line tool</b> draws lines from one point to another. Click and
50    drag across the display to draw a new line.</li>
51  <li>The <b>freeform tool</b> draws freeform curves. Click and
52    drag across the display to draw a new line.  <p>The freeform tool has several built-in editing features:
53  <ul>
54    <li>To <b>erase</b> a portion of a freeform, Ctrl+drag backwards along the
55      freeform from one end.</li>
56    <li>To <b>split</b> a freeform in two, Ctrl+click on a point along the
57      curve.</li>
58    <li>To <b>resume</b> drawing an existing freeform, click near the end of an
59      existing freeform and drag.</li>
60    <li>To <b>splice</b> two freeform curves together end-to-end, simply drag
61      near the end of an existing freeform while drawing.  A freeform in the
62      process of being drawn will automatically connect to a nearby end of an
63      existing freeform. When drawing freeforms close together, hold the shift
64      key to suppress automatic reconnection.</li>
65    <li>To <b>redraw</b> a portion of a freeform curve, click on the
66      curve and drag the mouse.  Dragging produces a tendril-like extension of
67      the curve.  When the tendril approaches the original curve, it
68      automatically reconnects, replacing the subtended segment of the original
69      curve.  To prevent the tendril from reconnecting to the original curve,
70      hold Shift.  Release Shift to allow the tendril to reconnect to
71      the curve.  If the mouse is released before the tendril reconnects, the
72      original curve is restored.</li> 
73    </ul> 
74  <li>The <b>marker tool</b> draws markers at a given point. Click a point in
75    the display to place a crosshairs there.</li>
76  <li>The <b>text tool</b> draws text at a given point. Click a point in the
77    display to place a new text object there, then type letters for them to
78    appear at that location.</li>
79  <li>The <b>oval tool</b> draws an ellipse. Click and drag across the display
80    to draw a new ellipse whose diagonal matches the path you draw.</li>
81  <li>The <b>box tool</b> draws a rectangle. Click and drag across the display
82    to draw a new rectangle whose diagonal matches the path you draw.</li>
83  <li>The <b>arrow tool</b> draws an arrow. Click and drag across the display
84    to draw a new arrow which stretches across the path you draw, with the
85    arrow's tip corresponding to the point at which you press the mouse
86    button.</li>
87  <li>The <b>polyline tool</b> draws a segmented curve, point-to-point.  Click
88    on the display to begin a new polyline.  Move the mouse and click to add
89    new nodes to the line.  To complete a polyline, double-click on the
90    display.   
91    <p>Like the freeform tool, the polyline tool has several built-in editing
92    features:
94    <ul>
95      <li>To <b>reposition</b> a node of a completed polyline, move the mouse
96      over the node until a green circle appears.  With the green circle
97      visible, click and drag the node to the desired postion, then release the
98      mouse.</li>
100      <li>To <b>delete</b> a node of an existing polyline, position the mouse
101      over a node until a green circle appears around it.  Then Ctrl+click to
102      delete the node.  The polyline splits in two around the deleted node;
103      however, any one-node polylines created as a result are automatically
104      deleted.</li>
106      <li>To <b>resume</b> drawing an existing polyline, move the mouse over an
107      end node so that a green circle appears.  Then click to resume drawing
108      the line at that end.</li>
109     </ul>
110  </li>
114To use a tool, click the associated tool button.
116<br><h3>Altering existing overlays</h3>
118You can use the overlays controls to alter the characteristics of selected
119overlays. First use the pointer tool to select the overlays you wish to change,
120or select them from the overlay list on the left side of the "Overlays" section
121of controls. Note that the overlay list only shows overlays for the current
122dimensional position.
124<p>To remove an overlay, click the "Remove" button or press the Delete key. 
126<p>To copy overlays to the clipboard, first select them, then click the "Copy"
127button or press the Ctrl+C key combination.
129<p>To paste overlays from the clipboard onto the current image plane, click the
130"Paste" button or press the Ctrl+V key combination.
132<p>To change an overlay's position, click and drag it using the pointer tool,
133or type in new values directly for the (X1, Y1) or (X2, Y2) coordinate values.
135<p>To change the text shown for a Text overlay, click the text object to select
136it, then type new text, or type new text directly into the "Text" box.
138<p>To change the color of the selected overlays, click the button labeled
139"Color" to bring up a dialog box for choosing a new color.
141<p>Some overlays--ovals, boxes and arrows--can be filled in (solid) or
142outlined (hollow). To toggle which for the selected overlays, use the "Filled"
145<p>Each overlay allows you to store one line of miscellaneous notes. To make a
146note for the selected overlays, type your note into the "Notes" text box.
148<br><h3>Grouping overlays</h3>
150Each overlay has an associated group. This feature is useful if one collection
151of overlays tracks a particular phenomenon, while another collection of
152overlays tracks another phenomenon. In this case, each collection can be
153assigned to a different group to differentiate between the collections.
155<p>To choose the group to which the selected overlays belong, choose a group
156from the "Group" dropdown box. New groups can be created by clicking the
157"New..." button next to the "Group" box.
159<br><h3>Distributing overlays</h3>
161VisBio's distribution feature allows for linear distribution of an overlay
162across many consecutive image planes. By identifying starting and ending
163overlays, you can instruct the software to create a series of intermediate
164overlays between the starting and ending image planes.
166<p>First, decide on a series of image planes across which you wish to
167distribute an overlay. For example, you could decide you want an oval overlay
168on slice #5, from timepoints #3 through #57.
170<p>Navigate to the first image plane and draw the overlay. In our example,
171create the oval at slice #5, timepoint #3.
173<p>Copy the overlay to the clipboard by clicking the "Copy" button (or by
174pressing the Ctrl+C key combination).
176<p>Navigate to the last image plane and draw the same type of overlay (or paste
177the copied overlay onto the exact same coordinates using the "Paste" button, or
178by pressing the Ctrl+V key combination). In our example, create or paste the
179oval at slice #5, timepoint #57.
181<p>Finally, click the "Distribute" button. To see what VisBio has done,
182navigate through the intermediate frames. In our example, move the Time slider
183between #3 and #57 to see how VisBio has distributed oval overlays.
185<br><h3>Changing the font</h3>
187Each set of overlays uses a particular font to display text overlays. The font
188being used is shown in the "Font" text box. To change it, click the nearby
189"Change..." button. A dialog box will pop up allowing you to select a new font.
190Please note that this setting affects all text overlays in the set, not just
191the selected ones.
193<br><h3>Saving your work</h3>
195<p>You can save your overlays to a tab-delineated text file on disk (readable by
196spreadsheet applications for further analysis). Click the "Save overlays..."
197button to do so, and a file browser will appear.
198The tabs on the right side of the file browser allow you select which overlay statistics you would like saved in the spreadsheet file.  <i>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.</i>
200<p>You can restore saved overlays by using the "Load overlays..." button and
201choosing a text file saved earlier. Please note that loading an overlay set
202will clear out any current overlays, overwriting them with those saved in the
203text file.
205<p>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.
208<br><h3>See also:</h3>
211  <li><a href="add_data.html">Add a data object</a>
212    - to create derivative data objects</li>
213  <li><a href="display_data.html">Displaying a data object</a>
214    - to visualize a data object</li>
215  <li><a href="data_transforms.html">Data transforms</a>
216    - for an overview of data objects</li>
217  <li><a href="data_panel.html">Data panel</a>
218    - controls for managing data</li>
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