ImarisVantage - Visualize Microscopy Data in 5D | Imaris
 

ImarisVantage

Welcome to a new era of data interpretation, plotting and presentation. This module enables you to compare and contrast experimental groups by visualizing your image data (segmented and original) in five dimensions as uni- or multi-variate scatterplots. Along with the use of box + whisker (5-number summary) plots Vantage will help you interpret intrinsically complex and dynamic phenomena. ImarisVantage enables researchers to dissect their multi-dimensional, multi-object images by creating a series of fully customizable plots for better understanding of hidden relationships and associations between calculated measurements, objects or groups of objects.

  • Dissect multi-dimensional, multi-object images imags
  • Visualize your image data in 5 dimensions
  • Create fast, explorative and interactive multi-dimensional plots
  • Create side by side ready to publish one dimensional plots to compare groups
  • Export figures and annotations into your presentations

Created for Scientific Discovery

ImarisVantage is the perfect tool to explore differences between experimental groups (e.g. control vs test). It allows for the creation of interactive plots which help illustrate relationships/patterns/differences between objects or groups of objects. The users can produce informative and visually pleasing plots in which object data can be shown in multiple scalable dimensions overlaid with the original 3D volume data.

With multiple views at your disposal, you can turn your 3D and 4D data into a dynamic gallery of individual objects. Advanced time plots with Spots, Surfaces, Filaments and Cells can be created to display objects interactively as they undergo temporal changes. Furthermore, you can use ImarisVantage’s scatter plots to produce detailed and customized views of data in four dimensions with additional scaling and color-coding for better understanding of underlying connections between objects. Imaris Vantage also creates single-dimension scatterplots of univariate statistics from one or more image or group of images. This option enables easy, ready to publish comparisons of the distribution (median and quartiles) of a chosen calculated measurement from several groups of images.

All these analytical tools are now ready to use in ImarisVantage and similarly to other functions in Imaris, they use an intuitive Creation Wizard. It guides the user through the step-by-step procedure to create the desired visualization optimizing the final plot and the data presented within it.

In addition to these new powerful data visualization tools, all the data and views created in Imaris can be annotated with individual titles, captions, labels and other highlights for enhancing presentations or publications figures. Both custom text and calculated statistical parameters (require ImarisMeasurement Pro) can be used to label each detected object.

With a few clicks users can add an annotation label to a figure that highlights some detail of the image. Then users can choose which calculated measurement to display. Annotations are fully customizable, you can use different font styles and sizes as well as different styles and colors of arrows and text boxes which is just to mention a few from a range of possibilities for the annotations’ appearance. ImarisVantage allows figures to be exported as an HTML-file, which can easily be opened in most text processors or presentation programs. The image created in ImarisVantage can also be exported by creating a snapshot.

With ImarisVantage you can save the figures with the image data and with the camera or viewing position in 4D space associated for each figure for easy modification if needed.

Creation of Plots

Imaris Vantage was created having in mind the need to (a) quickly create explorative and interactive single- or multi-dimensional plots and (b) easily compare multiple groups of samples (e.g. control vs test1, test2…) within the Imaris environment.

  • Wizard-driven - Use ImarisVantage wizard to create multiple plots. Spots, Surfaces, Filaments and Cells can all be used as input objects for various plots.
  • Flexible - Choose from more than 20 possible plots – from single dimensional univariate plots, through a basic 3D data representation to an advanced time or scatter plots where each calculated measurement can be remapped in multiple dimensions – XYZ, time, color and scale.
  • Applicative - Represent multiple experimental groups and conditions within a single Vantage view for instantaneous and meaningful comparisons.
  • Intuitive - Modify your plots to highlight certain features of the dataset and combine plots from the same analysis, e.g. show Spots and Filaments in the same plot figure. Navigate easily between multiple plots created from the same dataset.
  • Precise – Modify and save plots’ creation parameters to reproduce them for similar data sets. Change attributes of rendered data in the Settings tab to update the plot display instantaneously.
  • Powerful – Take control of a vast array of plot options to tailor them to meet your exact analytical needs. Edit and view plots, align and scale objects, remap dimensions, overlay objects with original volume data. ImarisVantage has access to hundreds of calculated measurements available from Imaris MeasurementPro.

Navigation and choice of styles

  • Interactive - All plots created in ImarisVantage are interactive and can be viewed, rotated and navigated through just like any object in Imaris’ Surpass view. Similarly, all objects can be individually selected for closer examination and comparison of their associated statistical values.
  • Familiar - Use the plot’s Settings tab to modify the style and number of features displayed in your image. Existing Imaris users will find out this process is identical to changing style of Surfaces, Spots, Cells and Filaments; new users will quickly discover and learn how smoothly these parameters can be adjusted to their needs.

Numerical tables

The values behind all plots created in ImarisVantage can be found in the table underneath the main plot window. You can select objects in 3D space and delve into the statistical underpinnings of your scatter plot or gallery view. There are two tabs available for your convenience, Detailed and Summary (where the 5 number summaries associated with the box + whisker plots is displayed). All values used in plot’s creation process can be exported as a .CSV, .XML or .XLS file for additional processing outside Imaris.

Creation of Figures and Annotations

In addition to insightful plots, ImarisVantage allows for the creation of figures and annotations for presentations and publications with just a few clicks. It is as simple as that!

  • Figures - Create figures for any view of Imaris: each figure will store the current view.
  • Annotations - With a few clicks you can add an annotation label to a figure that highlights some detail of the image. Position the annotation by simply clicking and dragging, give it a title, and have it pointing to the detail of interest. The annotation box can be moved and resized at any time and the description area of the annotation can be closed or expanded as desired.
  • Statistical Annotations - For every object that has been segmented within Imaris, the user can add statistical annotations that are displayed in 3D space at individual time points of that object. Parameters like speed, acceleration, displacement, area, track length and volume can be easily included within the image to create a new figure. A few clicks will let you select an object or objects of interest, select one or more statistical parameter from the extensive statistics list, and ImarisVantage inserts the statistical annotation within the image.

Navigation and choice of styles

ImarisVantage provides an easy and convenient way to navigate within existing and saved figures. Choose from a range of style possibilities for annotation appearance to adapt output styles to requirements of the publication.

  • Save And Reload - Save the figures with the 3D image and then reload the figure at a later stage to modify the visualization if necessary. Change the color of the background or modify the point of view of the 3D scene for example.
  • Interactive 3D Navigation - The anchor point and the line of an annotation are dynamic and update as the user changes the view or the camera angle. This feature provides amazing usability when changing views or creating movies because the annotations never have to be realigned.
  • Search Function - Navigate to an annotation by selecting it in the list or perform a textual search for the annotation based on the title or a keyword.
  • Fonts – ImarisVantage offers the full range of different font styles and sizes available on your computer. You can also choose text color and format from a broad selection of possibilities.
  • Annotations - Different styles and colors of arrows and text boxes are available within ImarisVantage. These items may be turned on or off at the users preference.

Export of Figures and Plots

ImarisVantage provides the necessary tools to export figures and plots easily. Both can be seamlessly imported into your favorite word processing or presentation software.

  • Export Tab – The Export tab saves the figure as HTML file. Exported HTML includes snapshot with caption, annotations and image metadata. A plot’s numerical data can be exported as .CSV, .XML and .XLS file for further downstream processing.
  • Snapshot - The created figure or plot can be exported by creating a snapshot of the current view. You can also choose text color and format from a broad selection of possibilities.
  • Search Function - Navigate to an annotation by selecting it in the list or perform a textual search for the annotation based on the title or a keyword.

Creation

  • Create and manage plots and figures for any Imaris view.
  • Quickly prepare images and advanced, multi-dimensional visualizations for publication.

Source data

  • Input objects for plot creation process are Spots, Surfaces, Filaments and Cells from a single image or from multiple images or groups of images.
  • Multiple categories of objects can be selected to create multiple infograms within the same plot – e.g. Imaris scene with Surfaces and Filaments can be used to create one plot for surface objects and another one for filament data.
  • The same object category can be used multiple times to create different plots – e.g. same set of surfaces can be used for Gallery and Scatter plots.
  • Plot creation settings can be stored and recalled via "Load Plot Settings"

Type of plots

  • 1-D univariate plot – for side by side representation of the a chosen statistical parameter from one or more groups of images.
  • XYZ plot – maps objects of interest in 2D/3D spatial dimensions – it is identical with the Surpass view of the scene.
  • Gallery plot – maps objects in 2D matrix and places them in a grid of rows and columns. The objects can be sorted based on any calculated measurement.
  • Time plot – maps 2D/3D data containing time component.
  • Scatter plot – allows fully flexible remapping of 2D/3D spatial dimensions with user-selected measurements.
  • Color and scale – to highlight more complex changes of relationships of objects’ measurements.

Creation of plots

  • Wizard-based selection of input data – spots, cells, surfaces and filaments.
  • Load plot settings – store and recall plot creation parameters.
  • Selection of plot’s type and plotted object’s category – surfaces, dendrite, edge, filament, point, cell.
  • Plot values – up to five, user-defined dimensions – XYZ, Color and Scale.
  • Box + whisker plot using the 5 number summary for each Imaris object added to the Vantage plot.
  • Show all time points – for 2D/3D + time datasets with Time mapped to one of the spatial dimensions.
  • Each object category can be interactively modified in their respective Settings/Color tabs for style, quality and color-coding (see Imaris -> Datasheet -> Visualization – Surpass View).

Properties of plots

  • Each object category shown in a newly created plot can be modified according to its Settings.
  • Sub Volume - in addition to Style/Quality controls, the user can show and scale in XYZ the original volume data overlaid on rendered objects.
  • Blend mode – use blend rendering to display original sub volume data.
  • Rebuild – re-do the plot creation process and/or input data selection
  • View - scale, rotate and align objects present in the plot.
  • Select – pick individual objects in the plot or in the numerical table below the plot area to highlight and inspect them.
  • Edit – reassign statistics to XYZ dimensions, color and scale (if applicable) – access the flexibility of ImarisVantage to fully customize your plot’s parameters.
  • Color – use color coding – base or statistics-related to code plot’s objects.

Vantage statistics datasheet

  • Numerical data used to create each plot is located underneath the main plot window.
  • Detailed tab: shows all the values for the measurements used in any given plot and for each object plotted.
  • Summary tab: shows the 5 number statistical summary for each object group present in the plot and for each measurement plotted.

Statistical Annotations

  • Display the statistical value of any segmented object as an overlay on the image in 3D space.
  • Choose one or more values to display from all the statistical parameters that are calculated by ImarisMeasurementPro.
  • Show the statistical values overlaid on the center of the segmented object and / or within the annotation text box for that object.
  • For objects that have statistical values that change over time, the statistical values also change as the user scrolls through time or as the user creates an animation over time.
  • Use statistical annotations at different time points to highlight the key stages of your object’s travel and behaviour.

Exporting data

  • ImarisVantage plots and figures can be exported and used outside of Imaris.
  • Figures - as HTML file with snapshot including captions, annotations and image metadata (figure title converted into caption title and figure text into caption text).
  • Plots – as numerical data in .CSV, .XML and .XLS file for further downstream processing.
  • As a snapshot for easy insertion in text or presentation software.

Visualization

  • Contains two main parts, a figure and an annotation
  • Figures are composed of annotations or symbols, a 3D attachment site and text.
  • A figure can contain zero, one or more than one annotation.
  • The annotations are the actual labels displayed in an image and can be added to any figure.
  • Within a figure the Imaris current view and the camera position are stored.
  • 2D annotations and symbols provide optimal reading.
  • The attachment point and the lines are updated with change of view or the camera angle.
  • Contents, location, size, the description area, fonts, formats and style can be adjusted in the annotation box.
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