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ImarisCell is an Imaris module specifically designed for the analysis of 2D, 3D, and 4D images of cells and their components. ImarisCell enables researchers to qualitatively and quantitatively examine micro relationships that exist between cells.

  • Examine relationships between cells and cellular components
  • Utilize biologically meaningful image analysis units
  • Detect cells based on cytoplasm or plasma membrane labelling
  • Detect and classify vesicular objects of various populations
  • Analyze cells in biological space - 2D to 4D



Making Sense Out Of Your Cell's Relationships

All known living organisms are composed of cells.  ImarisCell now allows you to use this natural and universal unit when doing your image analysis work. ImarisCell can identify individual cells in addition to their nuclei and multiple populations of intracellular vesicular objects.

You can now detect cell membranes not only when the cytoplasm is labelled but also when the plasma membrane and nucleus are labelled. Imaris Cell offers three distinct Cell detection routines; one ideal for samples with a marker that highlights all or part of the cytoplasm and two other algorithms ideal for when only plasma membrane and nuclei are labelled.

With ImarisCell, the fundamental unit of analysis has changed from a single image to clusters of cells, individual cells, or components of cells. This evolution prevents unnecessary generalizations caused by the limitations of single image analysis and facilitates specificity at the biological level of detail dictated by your research.

ImarisCell goes beyond what other image processing programs can do by using the biologist's concept of cells and applying topological constraints on the detection of organelles. It encapsulates Bitplane's powerful image analysis algorithms and simple yet high-level creation wizards to manage the detection, display and editing of multiple objects (i.e. Cells, Nuclei  and multi-class, multi--sized Vesicles). As always, Bitplane provides an interactive 3D interface with real time previews, interactive sorting and object selection using: filters, graphs, statistics tables, or by selecting directly within the image.

ImarisCell provides the platform necessary for 4D analysis (tracking 3D structures over time) which allows changes in size, shape, intensity, and position to be examined between cells or between organelles within a cell. This provides researchers with the opportunity to examine communication mechanisms as well as mechanical and structural functions of cells and cell components.

Features and Benefits

Features Benefits
Analysis can be classically performed on the entire image
Analysis can be performed on a per cell basis i.e statistics for components within each cell
Analysis can be performed on a per component basis i.e. statistics on the individual components such as nuclei and vesicles
Analysis can be performed on combinations of objects that meet certain statistical criteria (see object / object relationships below)
Researchers segment the "cell" structure based on a cytoplasm or membrane stain. The cell component is required because if other structures are also segmented these additional structures must be related to the cell. The user can choose any color channel for this component.
The researcher has the option of segmenting the nucleus of each cell. Since a nucleus must belong to a cell it is essential to detect the nucleus and cell simultaneously. The nucleus can be segmented from a separate color channel.
The researcher has the option of segmenting vesicles. A "vesicle" for ImarisCell can be any foci-like structure within a cell. In addition to actual vesicles this ImarisCell entity could be used to identify vacuoles, lysosomes, nucleoli, centrosomes, etc. In addition to this functionality, ImarisCell offers an additional analytical capability with a new XTention. It allows for finding vesicular objects outside the cell and calculating the distance between them and the cell. Because these components are related to the cell, it is essential that they are detected at the same time as the cell. Vesicles can be segmented from the same color channel as the nucleus or cell or a different color channel.
The Nucleus Biologists understand that a cell is a container which is defined by a membrane. The Nucleus of the cell must reside within this container. However, during imaging it is often possible to have very limited staining of the membrane immediately surrounding the Nucleus. This would cause the Nucleus, if it were near the edge of the membrane, to appear outside of the Cell, which as biologists we know is typically not possible in living cells. ImarisCell provides several options to correct this:
Expand the Cell area to contain the Nucleus
Reduce the Nucleus to be within the area defined as the Cell
Many types of cells should only have one Nucleus. ImarisCell provides an option to eliminate other objects detected within a single cell as nuclei so that there is only one nuclei per cell. This is a huge benefit when nuclear staining is poor.
In cases where Nucleus appears to be outside a cell it can be removed from analysis by selecting this option during the Cell object creation. This ensures that only real nuclei enclosed with cells are considered for analysis that may be focused on data like nuclear envelope volume or area.
Closely clustered nuclei that belong to different cells may pose an analytical problem if both nuclei are wrongly allocated to one cell. You can now split such nuclei by nucleus seed growth process that ultimately separates both objects.
Cell Creation Wizard Split Cells by Seed Points – Cells that are clustered together and lack a clear nuclear signal may be difficult to segment. In such case it is possible to differentiate between and ultimately produce individual cell objects by splitting cells by cell seed growth process that separates these objects.
Cell Creation Wizard Fill holes in Cell and Nucleus If a Cell or Nucleus object you wish to analyze contains interior holes you can eliminate them quickly, while still retaining the existing object segmentation. The filling is accomplished by setting the voxel in each hole set to a new intensity value, threshold value, and assigning them to the surrounding object thus closing the hole inside the Cell or Nucleus object.
Detect and visualize vesicles that belong to different populations sub-cellular organelles typically contain various vesicular structures that belong to different functional categories. They fulfill different roles and it often can be advantageous to discern different populations, or pools, of intracellular vesicles. ImarisCell offers this capability and allows creation of separate Spot objects corresponding to various classes of vesicles. Within each class vesicles can have a range of diameters (i.e. the diameter of each vesicle can be determined automatically by directly utilising the intensity and volume information in the raw image).
Each ImarisCell component can be color coded with any calculated statistical value.  This allows researchers to quickly and easily show in a visual manner complex relationships between cell components or their size, shape, or behavior.
ImarisCell components can also be exported to Imaris where additional visualization options are available. Cells and Nuclei can be exported as surfaces thus providing access to all available options in the surpass view. Likewise, vesicles can be exported as spots.
The standard snapshot and animation functions of Imaris can be utilized to produce stunning visual output of the resulting analysis of ImarisCell images.


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