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Start Off with ImarisVantage

ImarisVantage is a statistical data-visualization module, providing tools to create high-dimensional colour plots and analyze multi-object images. Its interactive visualization methods help you to enhance the understanding of complex statistical data by creating plots using actual segmented objects. The position of the object within the plot indicates the relationship between the selected statistical variables.

All created Surpass objects: Spots  , Surfaces  , Cell , and Filaments  could be used to create the Vantage plots. The object statistical data are used for the Vantage plot creation. To customize the list of statistical variables click on the Preferences icon  under the Statistics tab . The Statistics window opens and there you can configure the list of statistical variables. The enabled variable values appear both under the Statistics tab  in the Surpass view and within the Vantage.

ImarisVantage has a five panels workspace: Plot Tool Bar, Plot Input Data Area, Plot Property Area, Plot Display Area and Plot Numbers Area.

Plot Toolbar

Plot Tool Bar contains two icons: one to create a new plot  and one to delete . Click on the Vantage icon  and a new Vantage plot is added in the Input Data Area along with a new Plot Creation Wizard in the Property Area. To remove unfinished or existing plots, click on the  icon.

Plot Input Data Area

The Plot Input Data Area displays a list of the available Vantage plots

Each Vantage plot is organized in a tree-structure hierarchy. At the top of the hierarchy is the Vantage plot and all source objects are listed below. Each tree element has a check-box that controls the plot or object visibility.

Plot Property Area

To create a new plot, start with the Plot Creation Wizard.

The creation wizard guides you step by step through the process of selecting object categories, source data, plot type and the various dimension options. In the first step of the creation wizard, select an object category and source data. The category buttons allow you to choose the object type for the Vantage plot creation. According to the selection, all available source objects are listed. Select one of the input components from the list ( Spots, Surfaces, Cell, or Filaments) and the tree and plot are also interactively updated. In the next step of the creation wizard you can select the plot type you want to create.

Vantage lets you choose from four different plot types: XYZ , Gallery , Time  and Scatter . Once you have determined what plot type you want to use, several plot subtypes are available based on the chosen number of plot dimensions. XYZ, Time and Scatter Plots can show 2D or 3D plots with additionally assigned Scale and Colour plot dimensions.

Under the Plot values, you can assign the variables up to five plot dimensions. To select the statistical variable to be assigned to the chosen plot dimension, click on its name and the selected variable will be automatically assigned.

Selecting the Show all time point box displays all objects for all time points.

The Show Box Plots option is selected by default, displaying the box plots within the Display Area. A box plot visually summarizes the data of the selected variable to a five-number statistical summary

In the Plot Property Area, each source object can be interactively modified for style, quality and colour under the Settings or the Color tab. Once the plot is created, you can find all parameters available for adjustments and modifications for the selected plot in the Properties Area. The parameters are grouped under different Parameter Tabs: Setting , Rebuild , View , Edit , Frame  and Color .

Plot Main Display Area

The Plot Main Display Area shows a variety of interactive plots of ImarisVantage providing you a quick and easy overview of your data statistics. Plots are highly interactive and allow you to explore the data in many ways. As in Surpass View, you can interact with the plots in a variety of ways. You can further examine your data with the pan and zoom functionality.

To select an object or group of objects Change from the pointer mode to the Select mode and clicking on it. Selecting the object in the Vantage plot highlights it in the Surpass mode as well as in the corresponding row of the Plot Numbers Area table. To select a group of objects, press Ctrl+ left click (Mac:Command-left click).

Plot Numbers Area

The data presented in the Vantage plots are displayed in the table in Plot Numbers Area. In the Plot Numbers’ Area two table types are presented: Detailed and Summary

In the Detailed table, all statistical values used for the plot creation are shown. It contains the chosen plot dimension, variable name and unit, followed by the relevant object information such as ID, Parent number and Surpass Object name. The actual values of statistical variables are listed in columns. The values in the Plot Numbers Area also provide interactive two-way selection. A click on an individual row of the Detailed table highlights the corresponding object in the plot.

The Summary table contains a five-number summary based on all values within the set of a selected variable. The table shows the most important percentiles: the minimum, the lower quartile -Q1, the median, the upper quartile -Q3 and the maximum the selected variable.. The Summary table is only available if during the creation wizard the Show Box Plots option is selected. The numerical data displayed in the Summary table are represented graphically within the Plot Display Area using box plots.

By selecting the Export icon , all of the data that appears in the Plot Numbers Area can be exported for further analysis either as Comma Separated Values *.csv, Excel file *.xls, or Excel XML *.xlm files.

ImarisVantage helps you illustrate relationships, uncover patterns, and interpret differences between objects or groups of objects within multiple data sets.

Date: January 2013

Category: Tutorial

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