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The Cell: An Image Library-CCDB – Tutorial Part 5

Posted in: Microscopy and Imaging

This is the fifth in a continuing series of tutorials on getting the most from The Cell: An Image Library-CCDB.

In this tutorial you will be introduced to the new Pivot View tool that gives you even greater control over the search and introduces a real image based search tool.

Pivot View

Pivot View is the newest tool for viewing and finding images in The Cell. Built using Microsoft Silverlight, it allows for a very visual viewing experience. Please note that you will need to have Microsoft Silverlight installed to use the Pivot View. The launch button for Pivot View is the button on the far right end of the browse bar:

The Cell: An Image Library-CCDB – Tutorial Part 5
Selecting this button will launch Pivot View. If you do not yet have Microsoft Silverlight you will be prompted to download it.

Once the collection loads you will see the whole Library in the center screen and the Cell Type option open on the left hand side navigation of the Pivot View window. Clicking each of the search categories toggles them open and closed.

The Cell: An Image Library-CCDB – Tutorial Part 5
There is a Keyword search category for common keywords or you can use the search terms box:

The Cell: An Image Library-CCDB – Tutorial Part 5
One of the major advantages of the Pivot View is the ability to select multiple terms under multiple categories.

For example, under cell type select astrocyte and Purkinje cell then under organism select Rattus norvegicus and Mus musculus. Once this is done go to the upper right corner of the Pivot View and select Sort order: cell type and grid view (the icon on the right);

The Cell: An Image Library-CCDB – Tutorial Part 5
This lets you visually compare the structure of astrocytes and Purkinje cells.

The Cell: An Image Library-CCDB – Tutorial Part 5
Switching the Sort Order to organism gives you a different view that allows you to examine the images for similarities or differences across the organisms.

The Cell: An Image Library-CCDB – Tutorial Part 5
There is some similarity in the views because the results for this particular analysis come from only a few different experiments.

The slider allows you to zoom in on the images.

The Cell: An Image Library-CCDB – Tutorial Part 5
Clicking a single image in the Pivot View zooms in on that image and provides basic information on the right hand side of the view. Clicking on the CIL number in the details will open a new tab with the detailed image page.

The Cell: An Image Library-CCDB – Tutorial Part 5
A single click returns you to your previous view.

Need a nice brain cell in the public domain for a news article or blog?!

Just select Public Domain under license and multipolor neuron under cell type.

The Cell: An Image Library-CCDB – Tutorial Part 5
Perhaps you are just looking for all the images in The Cell from the Olympus BioScapes Digital Imaging Competitions®? Use the Search box in the Pivot View and search for Bioscapes.

The Cell: An Image Library-CCDB – Tutorial Part 5
At The Cell we are very interested in how you use the Pivot Tool, whether it is simply to find images to use on your website or in lectures or whether you use it for research. Please let us know how you have used it and if it was successful for you by sending an email to David Orloff at dorloff@ncmir.ucsd.edu.

This tutorial is the fifth in a series.

The first tutorial described setting up and using a free account and can be found here https://bitesizebio.com/articles/the-cell-an-image-library-ccdb-tutorial-part-1/.

The second tutorial described various ways to interact with and find cell images and can be found here https://bitesizebio.com/articles/the-cell-an-image-library-ccdb-tutorial-part-2/.

The third tutorial showed how to use the Advanced Search feature to further pinpoint images and can be found here https://bitesizebio.com/articles/the-cell-an-image-library-ccdb-tutorial-part-3/.

The fourth tutorial further explained licensing issues and the use of ontologies for finding images and can be found here https://bitesizebio.com/articles/the-cell-an-image-library-ccdb-tutorial-part-4/.

What else would you like to see? Please email David Orloff at dorloff@ncmir.ucsd.edu with any questions or suggestions for other tutorials.

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