SIA (Semantic Image Annotator), v0.2

Semantic Image Annotator, v0.2 (beta)

User Guide

-SIA is an interactive image segmentation tool designed to allow curators of biological specimens to annotate image data with +SIA is an interactive image segmentation tool designed to allow curators of biological specimens to segment and annotate image data with ontology terms.

@@ -69,67 +69,80 @@ be accessed using the File->Open Recent 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.
+NOTE: You may also open images previously annotated in SIA. These files are marked with a .zip file extension and contain your previously-saved +segments, labels, and other annotation data.
Segmenting the Image
-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 Ctrl-click -). -

-If auto-segmentation is turned on (see Preferences), the image will be segmented automatically, with the foreground brightened and +Once an image file has been opened, you can segment +the image by drawing lines on it. +

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. +
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 Ctrl-click). +

+If auto-segmentation is turned on (menu bar: Toggle auto segment

), 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.

+If you are satisfied with the segmentation, you may click the Apply

icon to "form", or permanently affix, the segment. +

+Labeling Segments
+SIA has been integrated with ontology terms (currently provided by the Plant Ontology) to assist you in annotating your image segments. +After forming a segment, click on the Labeling Mode icon (menu bar:

) +and then search for Plant Ontology terms in the "Annotate" text box in the upper-right hand corner. After selecting a term, click the "Assign" button and your segment will be labeled. +If you want to perform more segmentation and labeling in your image, remember to first change your annotation mode by clicking +on the Segmentation Mode icon (menu bar:

). +

+Other Annotation Data
+You can supply a curator name, independent collection ID, and comments for each image. +You may also associate your annotated image with a taxonomic identifier. SIA uses the UBio Namebank Search taxonomy web service to provide you with +a searchable list of species. +

Undo, Redo and Clear
If you make a mistake, it can be undone by selecting Edit->Undo or -clicking the undo Undo Button

button in the +clicking the undo Undo Button

button in the toolbar. To redo, select Edit->Redo or click the -redo Redo Button

button. To -remove all forground and background markup, click on the clear Clear Button

button in the toolbar.
+redo Redo Button

button. To +remove all forground and background markup, click on the clear Clear Button

button in the toolbar.

Zooming
To get a closer look at the image, the toolbar can also be -used to zoom-in on the image. To zoom-in by 10% use the Zoom In

button. To zoom-out by 10% use -the Zoom Out

button. To +used to zoom-in on the image. To zoom-in by 10% use the Zoom In

button. To zoom-out by 10% use +the Zoom Out

button. To zoom the image such that it fits into the window without needing -scrollbars, use the Zoom Best Fit

-button. To restore the image to its original size use the Zoom Original

button.
+scrollbars, use the Zoom Best Fit

+button. To restore the image to its original size use the Zoom Original

button.

Brush Size
-To change the brush size, use the Paintbrush

button to show the brush size +To change the brush size, use the Paintbrush

button to show the brush size chooser. It is often useful to use a bigger brush to make markings more visible or to quickly mark up more pixels.

Views
It is sometimes useful to view the segmentation results in different -ways. The default selected view is called "Combined" and shows the -image, its segmentation highlighted and the scribbles all overlayed on -the same image. By using the drop down menu, you can select a different +ways. The default selected view is the "Combined" view; it shows the +image, its highlighted segmentation, and any current foreground and background markup lines...all overlayed on +the same image. Using the drop-down menu, you can select a different view:

Combined: Shows the image with foreground areas brightened and background areas -darkened. The foreground and background scribbles are overlayed.
Original: -Shows the original image, without any segmentation or scribbles -overlayed.

-Note: -Only the combined view displays the foreground and -background markup (scribbles). So if you are wondering where the -scribbles disappeared to, select the combined view to make them visible.
-
Saving and Exporting
-To save an work in progress segmentation, select File->Save. This -will save the current segmentation and markup as a context file (.ctx). When -finished segmenting an image, you may want to export the view as an -image. To export the current view select File->Export. -For example, if you wanted to save the segmentation mask, select the -mask view and then File->Export. -
+To save your work, select File->Save. This +will save all formed segments, ontology labels, and annotation data as a ZIP file (.zip), which +contains your previously-saved segments, labels, and other curation data. + +You may also want to export your annotated image as an HTML file for easy display on the web. +To export your current annotations as HTML-enabled images, check the box marked "Create HTML image map and open in browser" in the Save dialog box. +

+Requesting Features and Reporting Problems
+If you have an additional feature you would like to suggest, or if you have encountered any issues while using SIA, please send +us an email at <sia-support@palea.cgrb.oregonstate.edu>

diff --git a/Annotation/src/ie/dcu/apps/ist/Application.java b/Annotation/src/ie/dcu/apps/ist/Application.java index 25139e6..e8aa61e 100644 --- a/Annotation/src/ie/dcu/apps/ist/Application.java +++ b/Annotation/src/ie/dcu/apps/ist/Application.java @@ -19,7 +19,7 @@ import static ie.dcu.util.OsUtils.*; public class Application { public static final String APP_ID = "ist"; public static final String APP_NAME = "SIA (Semantic Image Annotator)"; - public static final String APP_VERSION = "0.2"; + public static final String APP_VERSION = "0.2 (beta)"; public static final String APP_RESOURCE_DIR = "resources"; /** -- 2.34.1