Annotating dimensions - Cytobank documentation
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  • Illustration Dimensions provide a way to order (and re-organize) files within an illustration.

     

    Cytobank uses information about your experimental files in order to create illustrations.  By telling Cytobank minimal information about your experiment setup, Cytobank enables you to create and reorganize figures easily.

     

    View results quickly:

    You can use the Filename dimension to get a quick view of the results.  This lets you see your data without having to annotate the details of the experiment.

     

    Create polished figures quickly:

    If you tag information about your experiment, such as how the cells were stimulated (Conditions), how long cells were stimulated (Timepoints), which patient is shown (Individuals), or what dose of an inhibitor was used (Dosages), you can then use figure templates that provide one-click figures.  An example of a one-click figure would be to show a dose response for an inhibitor titration and calculate the 50% inhibitory concentration (IC50).  The more information you add, the more you can do with your figure.

     

    If you annotate dimensions, you can also search for datasets based on experiment design.  For example, if you have uploaded several experiments where you stimulated cells with the cytokine IL-4 and wanted to find all the ones where you used 20 ng/mL IL-4, you can search for experiments where you annotated a Condition of "IL-4" together with a Dosage of "20 ng/mL".

     

    For public datasets, we recommend fully annotating the Dimensions of the experiment.  This makes it much easier for people viewing the experiment to understand the experiment design, purpose, and controls.

    The types of Dimensions in Cytobank correspond to common things measured in experiments (also known as "experiment variables").  These include:   Timepoints are specified durations used in your experiment. Most commonly, these are times which a sample was allowed to signal before being fixed, but timepoints ...
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    Dimensions that are not in use are shown in blue text within the illustration page.  When you first begin, most of the dimensions are blue, ...

    Open the dimension editor by clicking "Edit" within the dimension box on the illustration page.   Click on the tab for the the dimension member ...

    From the layout or placeholder illustration view, click the label for the dimension and drag and drop it to the desired spot.