Digital Anatomist Image Collection Manager Tutorial

Overview

The Digital Anatomist Image Collection Manager is a service that allows you to create and maintain a searchable archive of annotated images.  Some notable features are: 

• Hierarchical collections: You can organize your images into hierarchical collections, and assign them titles, descriptions, and other attributes.
• Custom display: control the size, sequence, and layout of images for optimal viewing purposes.
• Knowledge management:  You can create your own structured keyword lists, which will be available for assigning to images and collections, and which become part of the search interface.  You can also participate in the collaborative development of a global keyword list.
• Annotations: You can upload image maps that designate segmented regions of interest, which makes your images interactive.  Users will be able to click on a structure and see its outline and name.  
• Access control: You can control access to each of your collections, making them public, private, or accessible by a specified list of users.
• Custom Search: you can search for images on any number of attributes, including keywords, image type, source information, or annotations.   

The simplest way to get started is to point your browser at the home page, then click on the "Public Images" button. This will show all image collections that have been created by other users, and which have been made available for public viewing by their owners. Follow the instructions in Browsing Collections below for accessing images in these public collections. If you want to create your own collections you need an account, which for now is as simple as signing up for one (see Getting an Account). After you have an account you can create and edit your own collections, add images, and make collections available to others.

Browsing Collections

You can browse collections by going to the home page and clicking on "Public Images", or by logging in and clicking on "My Collections" or "Other Collections".  Collections are arranged in a hierarchical structure: each collection may contain images and/or sub-collections.  There are three basic levels of interaction for browsing collections: the collection list, the individual collection, and the individual image within a collection. The following sections describe operations you can perform at each of these levels.

• Access an individual collection by clicking on the collection icon. You will then be at the individual collection level, described in the next section.
• Search for images.
  1. Enter text in the provided search box, and press "FIND".
  2. You will be shown all images that have titles, descriptions, or keywords that match your string.
  3. Save images from your search results to your hard disk by clicking on the image, right clicking on the image, then choosing Save Image As to choose a filename on your disk.
  4. Save selected images from your search results by clicking on the checkbox underneath each image, and then choosing a destination collection. Only those collections for which you have write access will be shown.
• Perform an advanced search.
  1. To search using structured keyword lists, annotations, image author, source information, or other attributes, click on "custom search". This option permits searching all collection lists available to you.
  2. Enter any combination of constraints, and press FIND.
  3. Images which match all your constraints will be displayed.

• Access an individual image by clicking on the image icon. You will then be at the individual image level.
• View metadata (keywords, etc) by clicking on "View Metadata".
• Change the size and layout of images when viewed as a group  
  1. Click on "Image Options".  
  2. Modify the size of the image icons by clicking on one of the size links (thumb, small, medium, etc.).
  3. Control the number of images per row by clicking on one of the numbers next to "Columns:".  
  4. The layout you select will remain in place until you change it or log out.
• Use slide-show mode to view images with minimal distractions on the screen, such as for presentations.
  1. Click on "Slide Show"
  2. Click on Next or Previous to cycle through the images in the collection.
  3. Exit slideshow mode by clicking on the collection name.
  4. Access an individual image by clicking on it. If there are no annotations associated with the image you will be taken to the individual image level where you can change the size of individual images. Otherwise the annotations will be displayed.

•  Change the size of individual images.
  1. Click on your preferred size.  The "as submitted" selection will present the image in its original dimensions.
  2. The image will resize according to your selection.  A smoothing transform is performed to assure quality image viewing. 
  3. The size will remain in place until you change it or log out.
• Interact with an annotated image.
  1. Hover your mouse over the image.  When you see it change from an arrow to a hand, you are in an annotated region.  
  2. Click on an annotated region, and the image will be redrawn with the annotated region outlined.  If the region has a name assigned to it, you will see the name at the top of the image.
• Navigate to other images in the collection.
  1. Press Next to go to the next image in the collection
  2. Press Previous to go the the previous image
• Enter slide mode by clicking the "Slide Mode" link
• View information about the image by clicking the "View Metadata" link
• Copy an image to another collection.
  1. Click on "Copy Image".  
  2. Select a destination collection that you have write permissions to, and press "COPY IMAGE".  
  3. Note: you will be copying the image only and not its metadata. If the original image is deleted, your copy will not be affected.
• Save the original image to your local disk for use in personal presentations or publications
  1. Click on the link "Retrieve original"
  2. Click Save To Disk in the warning dialog that pops up
  3. In the Save As box navigate to the subdirectory in the file tree where you want to save the file, and replace the Location field (which currently has "image-retrieve-original.pl") with the image filename. The extension should be the same as the original extension shown in the Retrieve original link. In fact the simplest is to just use the filename and extension shown in the link.
  4. Click OK
• Save a web viewable version of image to your local disk for use in personal presentations or publications. This operation will save the jpeg version of the original or reduced image to disk, as can be done with any image viewable in a browser. Note that this is NOT the original image.
  1. Right click on the image
  2. Choose Save Image As from the browser menu
  3. Choose a filename on your local disk and click OK

Getting an Account

If you want to create and edit your own image collections you need an account. Currently, anyone is allowed to set up an account. If this system becomes widely used we expect to restrict accounts to University of Washington and WWAMI users.

1. Point your browser to the home page. You can always return to this tutorial by clicking the Help link at the top of each page.
2. Click on Sign Up
3. Pick a username & password, and enter your name and email address.

You can now log in using your password.  At this point you will see a page showing collections that you have previously created (initially empty). A link will also show "Other Collections" that are available to you.

Creating & Editing Collections

• Create a new collection:
  1. Sign up for an account if you have not yet done so, and then log in.
  2. From your "My Collections" page, click on "create new collection".  
  3. Enter descriptive information, such as title and description. 
  4. You can make your collection a subcollection by choosing a destination parent collection. 
  5. When you are ready to create the collection, press "CONTINUE". 
  6. Once the collection is created, you can edit it at any time by clicking on "Edit Collection".
• Add images to your collection.
  1. From the "edit collection" screen, click on "Add Images".
  2. For each image you want to upload, press "BROWSE" and indicate the location of the image on your local disk. Most image types are supported. The filename extension is used to determine the image type, whch may cause problems for Mac users (haven't tested yet).
  3. Add optional captions to your images.
  4. Press SUBMIT.  The images will be uploaded.
• Choose a new representative icon for your collection.
  1. From the "edit collection" screen, find the image you want to appear as the representative icon for that collection.
  2. Click on "make this the cover image".
  3. Press SUBMIT.
• Reorder images as desired.
  1. From the "edit collection" screen, decide which images you want to reorder.
  2. For each image that will be moved, enter a new Order number
  3. You may use decimal points to indicate locations between other images. For example, to move image 3 to a spot between 5 and 6, you can type in the order number 5.1.  
  4. Press SUBMIT.   The images will be reordered, and their sequence numbers will be normalized.
• Delete unwanted images.
  1. From the "edit collection" screen, decide which images you want to delete.
  2. For each image that will be deleted, click the "Delete" checkbox under the image.
  3. Press SUBMIT.  The images will be removed.

Editing Images

• Edit the metadata for an image.
  1. You may only edit the metadata of images that are in your collections, or that you have been granted "writable" access to.  
  2. Navigate to the image and select "Edit image metadata".  
  3. Edit the caption and description, and assign any attributes through the drop-down menus and other form elements. Note these attributes are initially optimized for anatomy teaching. Additional attributes can be added as the system evolves.
  4. Press SUBMIT.
• Assign keywords to an image.
  1. You may only edit the metadata of images that are in your collections, or that you have been granted "writable" access to.  
  2. Navigate to the image and select "Edit image metadata".  
  3. Use the Keywords Manager to check the boxes next to the keywords you want to assign.
  4. You may enter new local keywords, which will become part your local keyword lists.
  5. You may enter new global keywords, which will become part of the collaboratively-authored keyword space.
• Assign annotations to an image.
  1. Create an image map using a standard HTML image map authoring tool, or create an IML file. IML (Image Markup Language) is an XML-based markup language created by Bill Lober for annotating images. More details about IML, and an IML authoring tool called AnnoteImage, are available at Bill's website
  2. If you are using an image map, the annotation names should occur in place of the URLs.  
  3. When the annotations are ready, first add the image itself to a collection by uploading the image file.
  4. From the image view page, select "upload annotations file".
  5. Follow instructions to upload the annotations file.  Indicate whether it is IML or HTML.  
  6. The annotation file will be parsed and integrated into the repository.  
  7. The image will immediately become live with annotations.
• Reset annotations for an image.
  1. If you need to change the annotations, use your external authoring tool to edit the image map or IML file.
  2. Upload the new annotation file.
  3. The old annotations will be overwritten.
  4. There is currently no way to edit a single annotation in place.

Access Regulation

• To regulate access to a collection: 
  1. Click on "Edit Collection".  
  2. Select a permission setting for "viewable by" and "writable by".  You may select PRIVATE (you only), PUBLIC (anybody), or a specific permissions group.
  3. Press SUBMIT.
• To grant or revoke permissions to a permissions group:
  1. You must have ADMINISTRATOR privileges to perform this function.  If you don't have it, ask the service administrator to do this for you.  
  2. If you do have ADMINISTRATOR privileges, Click on Options, and select "grant or revoke permissions".  
  3. Select a permissions group. 
  4. Use the checkbox interface to grant or revoke membership to this permissions group, and press SUBMIT.
• To create a new permissions group:
  1. You must have ADMINISTRATOR privileges to perform this function.  If you don't have it, ask the service administrator to do this for you.  
  2. If you do have ADMINISTRATOR privileges, Click on Options, and select "grant or revoke permissions". 
  3. Enter the name of the group to create.
  4. Assign membership with the checkbox interface, and press SUBMIT.