Interactive Segmentation Tool

SIA (Semantic Image Annotator), v0.2

User Guide

Usage

-In this section I will outline how to perform typical operations using -the tool, such as opening images, extracting objects and exporting -segmentation masks.
+SIA is an interactive image segmentation tool designed to allow curators of biological specimens to annotate image data with +ontology terms. +

Open an Image
-To open an image, select File->Open. Recently open files can +To open an image, select File->Open. +Recently opened files can 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.

-Select a Segmenter
-There are several different segmenters available in the tool. These can -be selected from the Tools -menu. To select one, -click on it.
-
Segmenting the Image
-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 Ctrl -and click instead of right click.
-
-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.
+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 +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.

Undo, Redo and Clear
If you make a mistake, it can be undone by selecting Edit->Undo or @@ -114,7 +106,7 @@ 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, 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:

Original: Shows the original image, without any segmentation or scribbles overlayed.
Markup: -Shows only the foreground and background markup (scribbles).
Mask: -Shows the segmentation mask. That is, an image such that the foreground -area is completely white and the background area completely black.
Foreground -Only: Removes all background elements and displays only -the foreground object.
Outline -Overlayed: Displays and outline of the object overlayed -onto the original image.

Note: Only the combined view displays the foreground and @@ -142,28 +123,15 @@ 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 or File->Save As. This +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.
-
-Configuring a Segmenter
-Some segmenters have parameters and options that can are configurable. -To configure the selected segmenter, select Tools->Configure -Segmenter, or click the

button in the toolbar.
-
-Navigating Directories of Images
-To quickly jump to the next or previous image in the current directory -(the one containing the open image), use the Go->Next and Go->Previous menu -items.
-
-Experiments
-Experiment files can be opened using the Tools->Open -Experiment menu item.

- \ No newline at end of file diff --git a/Annotation/src/ie/dcu/apps/ist/Application.java b/Annotation/src/ie/dcu/apps/ist/Application.java index 738a61d..25139e6 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 = "0.1"; + public static final String APP_VERSION = "0.2"; public static final String APP_RESOURCE_DIR = "resources"; /** diff --git a/Annotation/src/ie/dcu/apps/ist/dialogs/SaveReminderDialog.java b/Annotation/src/ie/dcu/apps/ist/dialogs/SaveReminderDialog.java index e7e55ae..cc5359c 100644 --- a/Annotation/src/ie/dcu/apps/ist/dialogs/SaveReminderDialog.java +++ b/Annotation/src/ie/dcu/apps/ist/dialogs/SaveReminderDialog.java @@ -34,7 +34,7 @@ public class SaveReminderDialog extends Dialog { private static final String TITLE = "Save Reminder"; private static final String QUESTION = "Do you wish to save your work before closing this file?"; private static final String SAVE_TEXT = "Save now and then close this file:"; - private static final String NOSAVE_TEXT = "Do NOT save this file; just close it:"; + private static final String NOSAVE_TEXT = "Just close it (CAUTION: unsaved changes will be lost):"; private static final String CANCEL_TEXT = "Do NOT close this file:"; // Dialog buttons -- 2.34.1