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How to use statistical annotations in Imaris

Statistical annotations give researchers the ability to view and annotate segmented objects with any statistical value that has been calculated for that object (i.e. Size, Shape, Intensity, Position, Movement). The statistical annotations allow the researcher to explicitly show the calculated value right next to the object of interest. Statistical annotations are available for display in the 3D/4D image for Spots, Surfaces, Cells, Filaments, and Tracks. Like color coding objects with statistical values (see the September newsletter), statistical annotations provide researchers another powerful way to highlight statistics associated with an image or objects within an image.

Statistical annotations can be added to one, several or all objects in an image in any combination the user chooses. The user is not limited to an annotation of one statistical parameter per object, but can add as many statistics per object as they like. Creating statistical annotation with Imaris is fast and easy. Statistical annotations require the modules Imaris, Imaris MeasurementPro, and Imaris InPress.

The following example describes how to annotate images with statistical values:

  • Once an objects has been segmented as Spots, Surfaces, Cells or Filaments click on the object in the surpass object list.
  • In the Statistical tab (in the object properties area on the bottom left of the screen) choose the 'Detailed' Tab.
  • Select the objects you want to annotate by clicking on them in the statistics list or by clicking on them in the 3D view (you must be in select mode to pick the 3D view). To select multiple items press the CTRL key or for a range of items press the shift key. Your selected objects will be highlighted in both the list and the 3D view.
  • To enable the annotations simply click on the 'Statistical Annotation' button Annotation Icon
  • In the viewing area the statistical annotation appears.
  • The statistical annotation shows the name of the selected statistical parameter and its value.
  • If the image is a time series, the statistical annotation is visible in the viewing area for all time points. Selecting a statistical variable that changes over time creates a statistical annotation that consequently changes with time.

  • You will also notice that the InPress window is automatically opened on the right hand side of the Imaris Window.
  • This Inpress window shows that an annotation has been added to the image, indicated by the icons Annotation Icon (an annotation at one time point) or Annotation Icon (an annotation that changes over time) at the bottom of the window. Following the annotation icon is the name of the object (Spots, Surfaces, Cells, Filaments, or Tracks) and the ID number of the object (Circled in red for illustration below).
  • There are also three tabs within the Inpress Window that allows the user to change all aspects of the appearance of annotation and also the statistics that have been selected.

text tab Text Tab - To change the appearance of the annotation text

  • Select / Highlight the annotation you want to change in the Inpress list
  • IMPORTANT – First click with the mouse into the box indicated with the black arrow above (don’t enter any text)
  • Then change any of the parameters below such as font, size, formatting and color

style tab Style Tab - To change the appearance of the annotation market point

  • Select / Highlight the annotation you want to change in the Inpress list
  • The default marker is set as a white sphere
  • Click the "Sphere" box to change to change to an arrow or magnifier
  • Click the white box to change the color to any desired color

Annotation Tab - To add or remove statistical annotations

  • Select / Highlight the annotation you want to change in the Inpress list
  • Then check / uncheck the checkbox in front of each statistic you wish to show or hide
  • Click the Preferences Icon preferences icon to see additional statistics available

Date: October 2010

Category: Case Study

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