Imaris for Cell Lineage
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Imaris Cell Lineage

Imaris CL Package is perfect for researchers in several life science disciplines i.e. cell biology, immunology, cancer research, plant biology, embryology and development who require a broad range of functionalities to study living cells and organisms. On top of the full range of 3D/4D visualization and analysis methods, Imaris CL provides the functionality for smart cell based segmentation, analysis per cell basis and discovering intracellular relationships. The package includes advanced functionality for studying cell motion or embryo development providing tools for automated detection of cell divisions and and creation of interactive lineage tree.


Imaris core is an essential module which delivers all the necessary functionality for experiment data management, visualization and segmentation of the 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with multi-channel datasets from a few megabytes to multiple gigabytes in size. Multiple volume rendering and modes, clipping planes, cross-section slices will let you create stunning animations and snapshots ready to be used in publications.

  • Search, tag, and manage your data
  • Organize and manage full experiments
  • Use premier volume rendering in 3D/4D
  • Detect objects using Spots and Surfaces
  • Enjoy interactive and intuitive workflows

Imaris Cell

ImarisCell is designed for smart detection of cells based on cytoplasm or plasma membrane labelling. Cytoplasm, nucleus, nucleoli and various populations of vesicles can be detected and analyzed as a complete cell object. ImarisCell enables researchers to map organelles and other cellular components within individual cells and get measurements, such as number of vesicles, nucleus or cytoplasm volume or intensity etc. per cell basis. ImarisCell also allows researchers to examine the relationships between those components and between cells.

Imaris Cell
  • Utilize biologically meaningful image analysis units
  • Detect cells based on cytoplasm or plasma membrane staining (NEW cell detection algorithm available for membrane labelling only)
  • Detect and classify vesicular objects of various populations
  • Examine relationships between cells and cellular components

Imaris Lineage

ImarisLineage provides tools for accurate automated or manual tracking of all moving objects, including dividing cells. ImarisLineage enables creation of an interactive lineage tree where the cell fate can be traced from one progenitor cell to the final generation.

The lineage tree can be easily edited (connections between objects and branches, flipping branches) and every selected group of cells (e.g. cells coming from the same progenitor) can be labelled with a different name and color. Additionally, a range of statistic measures relevant for cell studies are included such as: Cell Cycle Duration, Generation, Time Since First Division, Time Since Previous Division.

  • Automatically track dividing cells in 2D/3D + time
  • Create interactive lineage tree (for Cells, Surfaces and Spots)
  • Use streamlined track/lineage editor
  • Label lineage tree branches with selected colors and names
  • Retrieve statistical measurements per labelled group of cells

Imaris XT

ImarisXT is a multi-functional two-way interface from Imaris to classic programming languages like Matlab, Python or Java enabling users rapid development and integration of custom algorithms that are specific and tailored to scientific applications where generic image processing would fail. Imaris XT enables free access to pre-existing library of XTensions available on Imaris Open which let you perform, i.e. : relative distance analysis between biological structures, quantifying the object-based colocalization of multiple vesicle markers, visualization and quantification of overlap region and contact area between two 3D structures.

  • 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

Imaris Vantage

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

Imaris Vantage
  • Create fast, explorative and interactive multi-dimensional plots with real objects
  • Define different variable for each of the 5 dimensions (x, y, z, colour, size)
  • Create side by side ready to publish univariate plots to compare groups
  • Export figures and annotations into your presentations
  • Get preview of the results of: Wilcoxon, T-test, F-test and Kolmogorov-Smirnov

Imaris Coloc

ImarisColoc has been designed to give tools to quantify and document co-distribution of multiple stained biological components in 3D or 4D datasets. ImarisColoc provides an array of statistical parameters that include the number of co-localized voxels, the % of dataset, ROI or channel that is co-localized. More importantly, ImarisColoc offers a choice of well-established co-localization coefficients: Pearson’s and Mander's.

Imaris Coloc
  • Multiple colocalization selection methods
  • Obtain statistics in real time
  • Present data as new 3D or 4D color channel
  • Expand or narrow the computed histogram region
  • Co-localization of entire time series analyzed in fewer steps

Measurement Pro

Imaris MeasurementPro enables researchers to extract critical statistical parameters from their microscopy images thus allowing for the quantification of scientific findings. Imaris MeasurementPro adds shape, size, and intensity based measurement capabilities to the volume rendering, surface rendering and object detection features of Imaris. It allows researchers to interactively classify, group, and filter segmented objects based on any of the calculated statistics. MeasurementPro enables 3D distance and angle measurements in your dataset.

Measurement Pro
  • Obtain, view and export statistics
  • Obtain precise measurements of intensity values
  • Define object-based coordination system to compensate for translational and rotational object movement during observation
  • Measure distances between points within an object


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.

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