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The Cell: An Image Library-CCDB – Tutorial Part 3

This is the third 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 http://microscopy.bitesizebio.com/articles/the-cell-an-image-library-ccdb-tutorial-part-1/.

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

In this tutorial you will learn how to use the Advanced Search to selectively pinpoint the images you for which you are looking.

Advanced Searching ‘The Cell’

Image Attributes

The ‘Advanced Search’ page gives users a number of ways to search and filter images in the Library.  In addition to keywords there are a number of ‘Image Attributes’ that can be used to find images.

 

A ‘Z-stack’ means…

To clarify some of these terms, a ‘Z-Stack’ is a set of images where each plane (each image) represents a different slice of a solid image in the Z dimension so moving through this stack of images is as if you were moving through the solid from front to back or vice versa.

A ‘Time Series’ means…

A ‘Time Series’ is a stack of images where each plane of image represents a different time point. This is like having each frame of a movie as a separate image to look at.

Using all the search terms at once

A very interesting thing to note is that all of these terms can be used at once and if multiple items are checked it uses the Boolean ‘or’. For example, if a user checks both ‘Z-Stack’ and ‘Time Series’, a search is run as ‘Z-Stack or Time Series’ so both types of images are returned. However, very interesting in this case is that the search also returns images that are also ‘Z-stack and Time Series’. These are images which are both three dimensional and a time series. This allows the user to move through the image in space and at each spatial plane, run a movie. In other words, the user can move through time and at any time point stop the movie and move through space.

A metaphor of this is to imagine a magazine where each page moves you through space, but on each page you can watch a video!

The search results can be further refined on the search results page with this feature found at the top of the search:

 

Note that all searches (both simple and advanced) show the results with the icons used in the ‘Image Attributes’. This is so that the user can see certain features of the images without having to open them, for example, whether it is a video or still. Note also that not having the ‘Video/Animation’ icon, the ‘Z-Stack’ icon, or the ‘Time Series’ icon means that it is a still image.

Seeking visually similar images

To further explain the other ‘Image Attributes’, the ‘Grouped’ feature lets the user select those images that have been grouped with others. This lets you seek those images that may have all come from the same paper or that are very visually identical.

Easy to find, but not confusing!

The images have been grouped in two ways in the Library, one way just makes it easier for the user to find related images and the other way reduces the number of visually extremely similar images by only presenting a representative image. This is done so that the user does not have to scroll through pages and pages of what look like the same image! These sets can be very useful to computational biologists and to researchers who perhaps want to test a pattern recognition algorithm.

The ‘Suitable for Quantitation’ selection is a way to search for those images that have been determined to be suitable for direct measurements and calculations.

In the next section of this Tutorial, we’ll look at Licenses and how to search using the three categories of scientific terms found in The Cell.

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