Imaris for Cell Biologists | 3/4D Image Visualization & Analysis Software for Cells and Tissue | Bitplane

Imaris for Cell Biologists

The Imaris for Cell Biologists package is ideal for researchers in several life science disciplines who require a broad range of functionalities to study cells and organisms. In addition to Imaris’ proven 3D/4D visualization and analysis tools, ability to simultaneously visualise multiple 2D, 3D or 4D images with differing spatial or temporal dimensions and resolutions, Imaris for Cell Biologists provides the functionality for smart cell based segmentation, analysis on a per cell basis and discovery of intracellular relationships. The package includes automated tracking, detection of cell division and creation of interactive lineage trees along with statistical tests and a two-way interface for customization in Matlab, Java or Python.

Automated detection of cells and organelles

Imaris for Cell Biologists provides multiple options to detect and model your biologically relevant structures via step-by-step wizards with a preview of the results at each point in the workflow.

Cells with Organelles
Membrane Labelling


Use Imaris Surfaces to precisely visualize and measure organelles, nuclei, biofilms, cells, tissues, organs, embryos as well as organoids:

  • Computer-generated representations of a specified region of interest in the data set
  • Can be calculated and visualized for data sets up to hundreds of gigabytes in size (technology available from Imaris 9)
  • Act as a container from which all the desired statistics can be calculated
  • Can be tracked in time (position, shape and intensity changes)

Tracking motion in real life conditions

Imaris for Cell Biologists is the most powerful commercial software for live cell tracking & analysis. It rises to the challenge of monitoring temporal changes in biological systems. Users have a choice of multiple sophisticated automatic tracking algorithms, manual tracking options as well as an intuitive and interactive track editing tool.

Tracking Motion
Nuclei Labelling
Tracking Cell Division and Lineage

Tracking motion in 3D or 2D

  • Automatically track objects of interest using one of the provided algorithms
  • Handle thousands of objects and time points
  • Represent trajectory or displacement using multiple visualization options
  • Calculate average and instantaneous speed, acceleration
  • Manually create and edit tracks

Statistics and measurements

After segmenting the image data Imaris calculates a wide range of statistics for all detected objects: Cells, Surfaces and Spots. All values can be used for color coding, plotted inside Imaris (using Vantage plots) or exported in an .csv or .xls file format. Parameters presented below are the most common statistic types needed by biologists. Imaris reports many more.

Motion Analysis

Average Speed
Instantaneous Speed
Track length
Cell cycle duration


Vesicles per Cell
Distance to Membrane
Vesicles per Nucleus
Distance to Cell Center


Number (count)
Position (x, y, z)
Distance between Spots
Distance to Surface object



Plotting, statistical tests and group comparisons

Imaris for Cell Biologists includes a seamlessly integrated tool to explore differences between experimental groups (e.g. control vs test) - ImarisVantage. It allows for the creation of interactive plots which help illustrate relationships/patterns/differences amongst object measurement or groups of objects and reveal hidden relationships.

Group Comparison
Statistical Tests


  • Turn your 3D/4D data into a dynamic gallery of individual objects
  • Compare shapes of your 3D detected objects placed next to each other within the grid
  • Select an object within the gallery view and check its position within the dataset

Visualization and animation export

Imaris provides a complete set of features for visualization of multi-channel microscopy datasets from static 2D images to 3D time series regardless of their size and format. Using Imaris for Cell Biologists users can:

  • Organize and manage full experiments including images and data analysis in Imaris Arena
  • Use premier 3D/4D volume rendering modes: (MIP, Blend, Shadow Projection, Normal Shading)
  • Benefit from Imaris’ high performance IMS file format which guarantees smooth navigation even in very large datasets (TB range)
  • Combine volume rendering, object representation, clipping planes and 2D slicers
  • Make high quality snapshots ready for presentations and publications in Snapshot Tool
  • Easily make animations which include volume rendering, detected objects, annotations and object motion by adding several frames of interest in the Key Frame Animation Tool

Further benefits of using Imaris for Cell Biologists

Imaris for Cell Biologist Package provides many more advantages and flexibility to experience complete analysis freedom during your experiments.

Image Data Management
Open-source Coding

Image Data Management


Arena – Organize Your Image Data into Logical Groups

  • Organize and manage all image data related resources (e.g. raw data, segmented results, image analysis protocols)
  • Organize your images into Assays and Groups to represent your experiment structure
  • Search all (or part) of your image related resources
  • Tag resources for easy searches and organization

Additional Resources

The Imaris Learning Center hosts a wide range of tutorial videos, how-to articles and webinars to guide you through the many features of Imaris. We have provided some links below which will get you started on some of our most recent developments.

Imaris Stitcher

Accurate and precise stitching of multiple tiles in XYZ is now possible with our big data capable Imaris Stitcher. Simply load 2D, 3D or 4D tiles for stitching and the software will detect their stage coordinates.


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