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-<h1>Interactive Segmentation Tool</h1>
+<h1>SIA (Semantic Image Annotator), v0.2</h1>
<h2>User Guide</h2>
-<h3>Usage</h3>
-In this section I will outline how to perform typical operations using
-the tool, such as opening images, extracting objects and exporting
-segmentation masks.<br>
+SIA is an interactive image segmentation tool designed to allow curators of biological specimens to annotate image data with
+ontology terms.
+<br>
<br>
<span class="section">Open an Image</span> <br>
-To open an image, select <span class="guicommand">File->Open</span><span class="guishortcut"></span>. Recently open files can
+To open an image, select <span class="guicommand">File->Open</span><span class="guishortcut"></span>.
+Recently opened files can
be accessed using the <span class="guicommand">File->Open
Recent</span> menu. Alternatively, an image file can be dragged
from your file system and dropped into the application to open it.
Currently images of type JPEG, PNG, GIF, and BMP are supported.<br>
<br>
-<span class="section">Select a Segmenter</span><br>
-There are several different segmenters available in the tool. These can
-be selected from the <span class="guicommand">Tools</span>
-menu<span class="guicommand"></span>. To select one,
-click on it.<br>
-<br>
<span class="section">Segmenting the Image </span><br class="section">
-Once you have an image open and a segmenter selected, you can segment
-the image by drawing scribbles on the image. First, move the mouse over
-the object you want to extract. Left click and drag inside the object
-to draw some scribbles inside the object. Now, move the mouse outside
-the object to some background pixels. Using the right mouse button,
-scribble outside the object to select some background. If using Mac
-OSX, or if you do not have a right mouse button (Graphics Tablet etc),
-you can use <span style="font-family: monospace;">Ctrl</span>
-and click instead of right click.<br>
-<br>
-The image will be segmented and the foreground will be brightened and
-the background darkened. If you are not happy with the segmentation,
-you can add more foreground and background scribbles.<br>
+Once you have an image open, you can segment
+the image by drawing lines on the image. First, move the mouse over
+the object you want to segment. Left-click and drag the mouse
+to draw a red line inside the object. This marks, or identifies, the foreground to be segmented.
+Next move the mouse outside of the object. Right-click and and drag the mouse to draw a blue line,
+marking the background (Mac OS X and tablet users: use <span style="font-family: monospace;">Ctrl-click</span>
+).
+<br><br>
+If auto-segmentation is turned on (see Preferences), the image will be segmented automatically, with the foreground brightened and
+the background darkened. If you are not happy with the segmentation, you may undo your mouse input (see next section)
+or add additional foreground and background lines to refine the segmentation.<br>
<br>
<span class="section">Undo, Redo and Clear</span><br>
If you make a mistake, it can be undone by selecting <span class="guicommand">Edit->Undo</span><span style="font-weight: bold;"><span style="font-weight: bold;"></span> </span>or
<span class="section">Views</span><br>
It is sometimes useful to view the segmentation results in different
ways. The default selected view is called "Combined" and shows the
-image, it's segmentation highlighted and the scribbles all overlayed on
+image, its segmentation highlighted and the scribbles all overlayed on
the same image. By using the drop down menu, you can select a different
view:<br>
<ul>
<li><span style="font-style: italic;">Original:</span>
Shows the original image, without any segmentation or scribbles
overlayed.</li>
-<li><span style="font-style: italic;">Markup:</span>
-Shows only the foreground and background markup (scribbles).</li>
-<li><span style="font-style: italic;">Mask:</span>
-Shows the segmentation mask. That is, an image such that the foreground
-area is completely white and the background area completely black.</li>
-<li><span style="font-style: italic;">Foreground
-Only:</span> Removes all background elements and displays only
-the foreground object.</li>
-<li><span style="font-style: italic;">Outline
-Overlayed: </span>Displays and outline of the object overlayed
-onto the original image.</li>
</ul>
<strong>Note:</strong><span style="font-weight: bold;">
</span>Only the combined view displays the foreground and
scribbles disappeared to, select the combined view to make them visible.<br>
<br class="section">
<span class="section">Saving and Exporting</span><br>
-To save an work in progress segmentation, select <span class="guicommand">File->Save</span> or <span class="guicommand">File->Save As</span>. This
+To save an work in progress segmentation, select <span class="guicommand">File->Save</span>. This
will save the current segmentation and markup as a context file (<span style="font-family: monospace;">.ctx</span>). When
finished segmenting an image, you may want to export the view as an
image. To export the current view select <span class="guicommand">File->Export</span>.
For example, if you wanted to save the segmentation mask, select the
mask view and then <span class="guicommand">File->Export</span>.
<br>
-<br class="section">
-<span class="section">Configuring a Segmenter</span><br>
-Some segmenters have parameters and options that can are configurable.
-To configure the selected segmenter, select <span class="guicommand">Tools->Configure
-Segmenter</span>, or click the <img style="width: 16px; height: 16px;" alt="Configure" src="icons/configure.png"> button in the toolbar.<br>
-<br class="section">
-<span class="section">Navigating Directories of Images</span><br>
-To quickly jump to the next or previous image in the current directory
-(the one containing the open image), use the <span class="guicommand">Go->Next</span> and <span class="guicommand">Go->Previous</span> menu
-items.<br>
-<br>
-<span class="section">Experiments</span><br class="section">
-Experiment files can be opened using the <span class="guicommand">Tools->Open
-Experiment</span> menu item.<br><br><br>
-<div class="footer">Kevin McGuinness 2008
+<br><br>
+<div class="footer">Orig. Kevin McGuinness 2008, Ed. Justin Preece 2012
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