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The Cell: An Image Library-CCDB – Tutorial Part 2

Posted in: Microscopy and Imaging

This is the second in a continuing series of tutorials on getting the most from The Cell: An Image Library-CCDB. The first tutorial described setting up and using a free account and can be found here.

Searching The Cell

There are a number of ways to find the cell images for which you are looking, and to interact with them. This tutorial will explain how to search with the interactive cell illustration, the browse bar, and the basic search. The next tutorial will explain and show you how to use The Cell’s extensive advanced search capability.

The Interactive Cell Illustration

The interactive cell illustration provides an interactive, visual interface to explore and learn about the cell;

The Cell: An Image Library-CCDB - Tutorial Part 2

By rolling over the image, various cell components and their corresponding label on the right hand side are highlighted. This feature also works by highlighting the word, revealing the highlighted cell component. As an example, see the image below showing the image as it looks when the mitochondrion is selected;

The Cell: An Image Library-CCDB - Tutorial Part 2

By clicking either the mitochondria in the image, or the text on the right, the user is taken to a special search results page;

The Cell: An Image Library-CCDB - Tutorial Part 2

This special search results page presents an additional level of interaction by not only showing a more detailed image of the mitochondrion, but the user can also interact with each cell component, allowing further exploration. Selecting any of these terms launches a search for images annotated with that term. In addition, a basic description of the mitochondrion is provided along with five ‘Related Molecular Functions’ and five ‘Related Biological Processes’. These are based on an analysis of the images currently in The Cell, and are links to searches for each particular function or process to further aid in research. In the realm of education, a significant aspect for students, educators, or researchers, is the connection between the abstract and the observed. Cell structure is often taught using illustrations which are abstract conceptualizations generalized for education. The Cell presents these abstractions alongside actual images (seen below the cell component illustration and the description) so that the user is actually exposed to the richness and variety, as well as the similarities, among and across cells and cellular components.

The Browse Bar

The browse bar seen here gives the user a very simple way to begin accessing the images in The Cell;

The Cell: An Image Library-CCDB - Tutorial Part 2

Selecting any of the terms in the browse bar takes the user to a results page that breaks down the images by category. These results initially show the categories in alphabetical order with a representative image, but with the tools on the page the user can adjust these results to better suit their needs.

On the search results page users will also find the browse results tool bar;

The Cell: An Image Library-CCDB - Tutorial Part 2These links toggle the search results. Sorting by image count will change the display so that the category with the most number of images is shown first. This will also replace the ‘Sort by Image Count’ option with a ‘Sort by Name’ option. Selecting ‘Hide Thumbnails’ removes the representative images and returns a text list of categories replacing the term with ‘Show Thumbnails’.

Some images are grouped together for a variety of reasons- perhaps they came from the same article, or were part of the same multi-panel image in an article. These images will have text on their detailed image page stating ‘This image is part of a group’and each image will be seen in search results. Selecting the link ‘group’ will take the user to a results page with all the images in that group. In other cases, to make for a more appealing interface for the user, images that are significantly visually similar are often presented in a group, but with only one representative image showing. This is to make sure users do not have to scroll through pages and pages of visually very similar image. These images will have- ‘This image is representative of a group of similar images’. Again, clicking the link ‘group’ will take the user to a results page with all the images in the group. Also note that the number of images shown when browsing counts the groups with a representative image as a single image. Users searching for groups of visually identical images to serve, for example, as sample sets to test pattern recognition algorithms can find them using the Advanced search (described in the next tutorial).

The Basic Search

The basic search box is found at the top of every page in The Cell;

The Cell: An Image Library-CCDB - Tutorial Part 2

One feature of the simple search is that as a user begins typing a search term, after three characters, the system will suggest terms to assist the user. For example, shown below is the screen showing the suggestions for terms that begin with ‘act’;

The Cell: An Image Library-CCDB - Tutorial Part 2

Only terms with corresponding images will be suggested to prevent the user selecting a suggested term and getting a null result. Also note that, when selecting from the suggested choices, quotes are automatically included in the search phrase. Users can still search for terms that do not show as suggestions. Note that to search, a user must click the Search button and not just press the return key.

As noted on the Search Help Page, there are additional tips to help users find the images for which they are looking.

Basic Search;

  • Use double quotes to restrict the search to an exact phrase, e.g. ‘basal body’ will locate images annotated with the two word phrase ‘basal body’ rather than the individual words basal or body.
  • You can combine words or phrases by using capitalized AND, OR, NOT- e.g. ‘basal AND body’ will locate images annotated with both keywords ‘basal’ and ‘body’. A search query using ‘basal NOT body’ will locate images that are annotated with the keyword ‘basal’ but not with the word ‘body’.
  • You can search for a particular image if you have its CIL id. Simply enter it in the basic search text box at the top- e.g. CIL:9776 (no spaces)
  • Bookmarking a search result will rerun that search on the current Library contents when you revisit.
  • If you email the search results link to yourself, clicking that link will rerun the search results on the current Library contents.
  • This tutorial is the second in a series. What else would you like to see? Please let us know, or email us with any questions or suggestions for other tutorials.
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