ImarisXT - Develop Custom Algorithms for Imaris | Imaris


ImarisXT is a multi-functional two-way interface from Imaris to classic programming languages, Matlab and other imaging software programs. It allows rapid development and integration of custom algorithms that are specific and tailored to scientific applications where generic image processing would fail.

  • Develop custom algorithms for image processing and segmentation
  • Answer challenging questions with targeted tools
  • Integrate new modules with a customizable user interface
  • Exchange data with Matlab, Java and Python
  • Free access to pre-existing library of XTensions

Revolutionizing Microscope Imaging and Analysis

Cutting edge research in biology, chemistry, or medicine requires advanced technology and in-depth understanding of specific processes. Model-based data analysis lies at the heart of today’s challenging research problems. Modern imaging products must be able to incorporate problem-specific know-how to automatically extract complex or subtle morphological or dynamic information.

Using Java technology it is possible to exchange image data (e.g voxel intensities) and derived image data (e.g. spot coordinates) from Imaris with another application. ImarisXT also offers a Plug-In for ImageJ and many useful XTensions (open source samples written in Matlab and Python).

With ImarisXT you can easily integrate your own algorithms for image processing, segmentation, classification, and reporting into Imaris by creating custom XTensions or Imaris can be turned into a dedicated visualization and interaction engine within a researchers host application. ImarisXT offers the most flexible solution for your cutting edge biological research.

Customize your analyses with ImarisXT now available on Windows and Mac OS systems.

The features of ImarisXT have been designed to facilitate the co-operation between biologists and computer scientists by providing each party with a specialized interface. Computer scientists will be able to work on the development platform of their choice, while the biologist will continue to work in Imaris. Biological labs will be able to cooperate with in-house computer scientists to develop task-oriented analysis modules. This ensures maximal efficiency and enables co-operation time to be utilized to discuss the specific aims and tasks of a joint project rather than the interface.

Custom Programming Interface

Imaris XT is a two-way communication between Imaris and various programming languages, to allow programming of image processing, segmentation, classification, or any other algorithm.

  • Java Interface - ImarisXT provides a Java interface to exchange image data and derived image data from Imaris with another application.
  • Programming Languages – Programming languages like Matlab®, Java® and Python® support easy integration of Java interface and can be used with ImarisXT
  • Application Programs - Increasingly popular and widespread, Java technology allows well-defined communication between different application programs.
  • COM Interface - ImarisXT's COM interface can still be used to exchange image data and derived image data from Imaris with another application, however it will not be further developed. Old, COM-based XTensions will continue to work but should you want to benefit from new ImarisXT functions, code migration to Java is required.
  • ImageJ Plug-In - Use readily available functions in the ImageJ software with the advanced visualization features of Imaris via an ImageJ plug-in that uses the ImarisXT interface

Data Exchange

ImarisXT allows the image data exchange as well as derived image data exchange via Java interface.

  • Image Data Exchange - Image data like voxel intensities, voxel size, channel description (name, color), time calibration, and image metadata can be exchanged between ImarisXT and external applications
  • Derived Image Data Exchange – Derived Image data like spot coordinates and diameters, surface objects (triangle coordinates), tracks (connections of spots and surfaces), filament graphs (coordinates, diameters), and new statistical values can be exchanged between ImarisXT and external applications

Customizable User Interface

ImarisXT provides a customizable user interface for seamless integration of new imaging modules (XTensions) into Imaris.

  • Image Processing Menu – ImarisXT offers custom written image-processing XTensions, which can be inserted into the image-processing menu of Imaris.
  • Surpass Tool Bar - Algorithms that create custom objects can be inserted as a custom surpass tool bar button.
  • Surpass Tool Tab - For algorithms that are directly related to or require existing Surpass components (spots, surfaces, filaments) the algorithm can be inserted in the “tools” tab of that component.


Program your own image processing and segmentation algorithms and share them with others if you wish.

  • Program – XTensions offer you the flexibility to answer challenging imaging questions with targeted and customizable tools while still working in the familiar Imaris environment.
  • Pre-Existing Library – ImarisXT users receive free access to pre-existing library of XTensions for commonly used data specific applications. These XTensions can be immediately used or can be used as a basis for custom code.
  • Exchange - XTensions can be exchanged peer-to-peer or can be made publicly available in Biplane’s XTension library.
  • XTension Lists - Lists are available for all XTensions for MATLAB and ImageJ.

Integrated Fiji/ImageJ plugins

Imaris provides Fiji/ImageJ compatible plug-ins aimed at performing additional image processing. Fiji/ImageJ offers a solution for specific problems with image analysis and boosts the analytical capability of Imaris.

  • Fiji/ImageJ is integrated into Imaris and can be executed from within the application.
  • Use your current Fiji/ImageJ routines while working within the Imaris structure
  • Enhance and extend the functions of Imaris with Fiji/ImageJ plug-ins
  • Use familiar ImageJ interface while doing analyses in Imaris
  • Customize the Fiji/ImageJ menu by integrating new plug-ins into Imaris - grow and expand your analytical capabilities
  • The list of available plug-ins is organized into familiar ImageJ menu structure. Each plug-in collection is displayed as a sub-menu on this list.


  • Java interface provides to exchange of image and derived image data from Imaris with another application
  • Multi-functional two-way interface from Imaris to both classic-programming languages (Java®, Python®) and to Matlab.


  • Imaris version
  • ImarisXT
  • XTensions installed with Imaris or downloaded from the website
  • XTension written in development environment supporting the Java interface

Transfer Data and linking Matlab and Imaris

  • Image Data
  • Spots Data (Positions, Radii, Tracks)
  • Surfaces Data (Triangles, Masks, Tracks)
  • Filament Data (Vertices, Radii, Edges)
  • Image Data Exchange
  • Voxel intensities
  • Voxel size
  • Channel description
  • Time calibration
  • Read/write image files in various formats

Data exchange

  • Java interface documentation is installed with Imaris
  • Customizable user interface
  • Extendable menu for image processing
  • Configurable surpass buttons to create custom objects
  • Customizable property tab for surpass components


  • The Similarity Statistic Values obtains the statistical characteristics of a selected object or objects to create an amalgamate of chosen values to identify the potential similarity among the other objects within the image.
  • The Camera Manager store and load an arbitrary number of viewpoints.
  • The FindSpotsCloseToSurface separate spots in an Imaris Spot component that are close to the specified surface.
  • The VesicleOutsideCell functionality calculates the distance between the closest cell and each spot object outside of the cell. This function may be applied to segment and quantify exo- and endocytotic vesicles involved in these processes.
  • The SplitSpot separates a collection of spots in distance specified groups
  • The SplitSpots Into SurfaceObjects segment a spots in multiple collections, surrounded by a surface object.
  • The Translate Track translated tracks relative to its start-point and shows the direction and distance of motion
  • The Spine Classification categorize spines based on spine statistics and shape (Stubby, Mushroom, Long, Thin)
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