AISO (Annotation of Image Segments using Ontologies), v0.3

User Guide

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

Open an Image 
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.

NOTE: You may also open images previously annotated in AISO. These files are marked with a .zip file extension and contain your previously-saved segments, labels, and other annotation data.

Segmenting the Image 
Once an image file has been opened, you can segment the image by drawing lines on it.

1. Move the mouse over the object you want to segment.
2. Left-click and drag the mouse to draw a red line inside the object. This marks, or identifies, the foreground to be segmented.
3. Move the mouse outside of the object.
4. 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 at least one foreground and background line have been drawn, AISO will segment the image automatically with the foreground brightened and the background darkened. If you are not happy with the segmentation, you may undo your mouse input (see "Undo, Redo and Clear" below) or add additional foreground and background lines to refine the segmentation. Edges in an image can be extracted wherever there is a detectable change in the lightness or darkness of adjacent pixels. The user may further refine their segmented area by adding foreground mark-up lines (red) outside of the initial area to expand the discernable boundary, or by applying background mark-up lines (blue) across the initial area to exclude nearby image content from the segment.

If you are satisfied with the segmentation, you may click the "Form segment" button to permanently affix the segment.

Labeling Segments
AISO has been integrated with ontology terms (currently provided by the Plant Ontology <http://www.plantontology.org>) 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. AISO uses the UBio <http://www.ubio.org> Namebank Search taxonomy web service to provide you with a searchable list of species.

NOTE: AISO currently requires an internet connection for the term label and species lookup web services to function properly. Your computer will need an active internet connection if you would like to use these features.

Undo, Redo and Clear
If you make a mistake, it can be undone by selecting Edit->Undo or clicking the undo button in the toolbar. To redo, select Edit->Redo or click the redo  button. To remove all forground and background markup, click on the clear  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 button. To zoom-out by 10% use the  button. To zoom the image such that it fits into the window without needing scrollbars, use the button. To restore the image to its original size use the button.

Brush Size
To change the brush size, use the 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 the "Segmented" 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:

• Segmented: Shows the image with foreground areas brightened and background areas darkened. Any current foreground and background annotation marks are overlayed.
• Original: Shows the original image without any segmentation or markup.

Saving and Exporting
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.

AISO Metadata File Structure
Any AISO-annotated image saved as a ZIP archive contains an XML file holding the user's curated metadata. The structure of this file is as follows (utilizing sample data):

<?xml version="1.0" encoding="UTF-8" standalone="no"?> <image_data> <aiso_version>0.3 (beta)</aiso_version> <orig_image_filename>sample_1.png</orig_image_filename> <species name="Chamerion angustifolium" ubio_id="478877"/> <curator_name>Chris Curator</curator_name> <comment>Sample annotation of a fireweed image.</comment> <collection_id>1</collection_id> <segments> <segment> <url/> <layer>1</layer> <annotation_term>anther</annotation_term> <annotation_id>PO:0009066</annotation_id> <polygon_coords>428,396,426,398...x3,y3,x4,y4...126,43</polygon_coords> </segment> </segments> </image_data>

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 AISO, please send us an email at <aiso-support@plantontology.org>