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. ImarisCell also allows researchers to map organelles and other cellular components within individual cells, then examine the relationships between those components.
Click here to view the ImarisCell Creation Wizard movie.
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.
The following features are available within ImarisCell:
Classically, microscopists have been forced to analyze their data on a per field or per image basis. They could count, for example, the number of cells in the entire image or the number of vesicles in the entire image, but could not easily count the number of vesicles in each individual cell when an image contained more than one cell. ImarisCell allows the researcher to determine which analysis unit they would like to use.
ImarisCell provides researchers with the ability to segment up to three different types of structures at the same time and allows those structures to be related to one another in 4D space / time.
ImarisCell takes biologists' knowledge about the appropriate structure of a cell and utilizes this during segmentation. This allows the program to deal with common problems associated with imaging cells and allows researchers to obtain more accurate results.
ImarisCell gives researchers the ability to examine complex relationships between cells, between cell components, or of components within a cell. This ability is derived from the fact that ImarisCell understands that a cell is a highly complex micro environment which includes both nuclei and vesicles. Therefore statistics can be generated on a per cell basis and spatial relationships within a cell can be determined. By utilizing ImarisCell's new concept of cell's components hierarchy, the user can export key statistical information about an object bearing a unique parent object ID. Analyzed vesicles or nuclei can now be easily allocated to its parent structure, i.e. it is possible to determine whether object of interest belongs to given Cell.
Utilizing the filtering and classification of ImarisCell researchers can begin to ask a series of advanced questions and receive answers to those queries. For example, ImarisCell could easily identify all the cells in the image where the various populations of Vesicles inside the Cell were close to the membrane and the Cell itself was moving quickly relative to the other cells in the image.
If users already have segmented datasets using existing Imaris components such as Spots and Surfaces or if users do not want to use the ImarisCell component for the segmentation because they are used to working with the other Imaris objects, they can still benefit from the power of ImarisCell. ImarisCell allows any Surface object (automatically, semi-automatically, or manually created) to be imported into ImarisCell as either a Cell or Nucleus. Likewise, any Spots object (automatically or semi-automatically created) can be imported to ImarisCell as a new vesicle type or as one of the previously detected types. This benefits users because they can utilize the wide range of segmentation functions in Imaris and still benefit from the object relationships report established in ImarisCell.
Because ImarisCell knows that the relationship between components of the cell is important for research and because it can make associations between components, it can therefore directly provide statistics that are important to biologists.
The location of vesicles within a cell can provide many clues about cellular function or functions of those vesicles within a cell. Therefore ImarisCell provides information on vesicle distance to; the closest nuclear wall, the center of the nucleus, to the edge of the membrane as well as the relative position within the cytoplasm or the nucleus.
(7) 4D analysis (3D over time) for all components
Cells are living entities and ideally researchers want to study them in the most realistic environment possible. This includes watching them in 3D space and longitudinally evaluating behavioral changes of the cells and their cell components. Not only can researchers track the cells themselves in 3D, they can track the movement of the nucleus and vesicles within each cell. The movement of these cell components is automatically corrected for the movement of the cell itself, so that the actual movement of the cell components within the cell is measured. As an example, movement toward or away from a membrane can be measured. Likewise, changes to the count, size, shape, and intensity of the cell components over time can be measured.
(9) Compatibility with ImarisXT
ImarisCell is fully compatible with ImarisXT. This means that researchers can use their own applications for advanced segmentation if they choose and then can import Cells, Nuclei, and Vesicles into Imaris to visualize the results and perform the analysis. Likewise, Cells, Nuclei, and Vesicles can be exported from ImarisCell with ImarisXT if researchers wish to do the analysis in their own application. ImarisCell is consistent with the other Imaris modules in allowing open exchange of image data, derived objects, and metadata between Imaris and custom programmed code.
Because ImarisCell is a module of Imaris it utilizes the same selection, classification, and interaction functions that Imaris is known for. Researchers can pick cells, nuclei, or vesicles right in the 3D visual view and immediately have the associated statistics highlighted in the table and vice versa. Imaris InMotion can be utilized for selection of what otherwise might be difficult to select objects in 3D space. The same object filtering and classification methods used in Imaris MeasurementPro can be utilized to select any cell component or specific sub populations of cell components.
-Vesicles of various classes and sizes (Optional)
- Excellent for large data sets to focus on areas of interest for fast processing
- Ability to apply set criteria to the entire dataset after ROI processing
- Settings are automatically set on a per image / channel basis
- Allows for processing large datasets after ROI processing without changing the parameters
- Ability to change a few parameters once result is seen
- All other parameters remain as previously set
- All settings for processing are recorded
- Non-Iterative (automatic):
- Automatic detection based on a seeded watershed routine. This algorithm also has an option (recommended) to “fill gaps on cell membrane”, which aims to minimize the adverse effects on the cell detection caused by heterogeneous plasma membrane labeling
- Use reiterative membrane boundary detection process
- Depending on membrane staining's distribution, select entirely smooth or piece-wise smooth detection algorithms
- Define, detect and isolate small membrane patches from analysis by removing tiny, detached membrane regions
- Select shape, length and curvature of the membrane's border during detection process
-Object detection does not depend purely on intensity
-Excellent for uneven staining or unevenly illuminated fields, bleached or fading samples, and thick specimens
- Split cells by seed point growing in the absence of nuclear stain signal
- Expansion of Cell - If the stained area for a Nucleus is outside of the stained area for the Cell the segmented area of the Cell can be expanded.
- Erase Nucleus outside of Cell - If the stained area for a Nucleus is outside of the stained area for the Cell, the nucleus outside the cell staining can be erased.
- Can enforce a limit of one nucleus per cell.
- Split clustered nuclei by seed point growing
- Excellent for independently segmenting otherwise touching objects
-Excellent for objects that are sphere like in shape
- Excellent for uneven staining or unevenly illuminated fields, bleached or fading samples
-Spheres - with user defined scale
–Total Number of Cells, Nuclei, and Vesicles in image
–Total Number of Cells, Nuclei, and Vesicles per time point
-Size: # of Voxels, Area, Volume
-Shape (Cells and Nucleus Only ): Ellipsoid Axis Lengths A, B, and C, Sphericity, Ellipticity; oblate and prolate
-Orientation (Cells and Nucleus Only ): X, Y, Z vector components for each Ellipsoid Axis A, B, and C
-Diameter (Vesicles Only) : Mean, Min, Max
- Position: Center of Image Mass and Homogeneous Mass in X, Y, and Z, Time Index
-Intensity: min, max, median, sum, std dev, and center on a per channel basis
- Bounding Box (object oriented and axis aligned)
– Number of Nuclei per Cell
– Nucleus to Cytoplasm Volume Ratio per Cell
– Number of Vesicles per Cell
– Intensity Mean, Min, and Max of all Vesicles within each cell
– Diameter Mean, Min, and Max of all Vesicles within each cell
– Cell Cytoplasm related (e.g. number of vesicles in cytoplasm)
– Nucleus distance to Cell Membrane
– Number of vesicles per Nucleus
– Distance from Vesicle to closest Nucleus border
– Distance from Vesicle to closest Nucleus center
– Distance from Vesicle to closest Membrane
– Relative vesicle position within a Cell
– Vesicle location within Cytoplasm
– Vesicle location within Nucleus
- Location of vesicle outside cell - distance from a spot to the closest cell (XTension - requires ImarisXT)
– Diameter of Vesicle (Mean, Min, and Max)
– Duration, length, straightness of tracks
– Displacement, X, Y, Z, total displacement, squared displacement of track
– Number of branches or fusions
– Quality of fit to autoregressive model- per-axis or mean of all axes of tracks
– Speed Mean, Min, Max and variation within a track
For Objects that have been tracked:
– Instantaneous velocity X, Y, Z, instantaneous speed, acceleration
– Average number of Nuclei and Vesicles within the cell being tracked
– Changes in the Object, Cell, and Vesicle specific statistics shown above over time
- Output movement of Nuclei and Vesicles relative to Cell - movement of these cell organelles is automatically corrected for the movement of the cell itself. This means that the cell movement is not obscuring the information on the intracellular traffic.
– Each object has a unique ID to identify it
– Object ID’s are shown in the statistics tab and in the output file
– Enter the ID number in the search field and search. The object is then highlighted (selected) in both the statistics list and the visual view
- Unique higher-level parent IDs are allocated to each cell object and the lower-level IDs of individual vesicles and nuclei are subordinate to that ID. Users can group segmented object that belong to a particular cell with the same parent ID.
Cells and Nuclei may be exported to Surfaces for expanded visualization
Vesicles may be exported to Spots
ImarisCell is completely compatible with ImarisXT allowing exchange of all ImarisCell components and derived data between Imaris and custom programmed code.
All visualization, snapshot, and animations functions of Imaris are available for ImarisCell objects.
- Pick any single or combination of objects from the visual view by clicking on them – the associated statistics are selected in the statistics tab
- Pick and single or combination of object statistics in the statistics tab and the associated objects are selected in the visual view
- Selection is completely interactive and real-time
- Choose any statistical parameter from a drop down menu
- Select in a histogram or type in values to include or exclude
- Objects meeting the selection criteria are automatically and interactively shown in real time in the visualization of the image.
- Combinations of statistical parameters may be used to filter on multiple criteria
- Grouped objects can have global properties applied to them such as color and transparency
- Statistical output can be exported only from a single group – See Statistics Output
ImarisCell features automated methods to identify, segment, trace, classify and analyze Cell, Nucleus and Vesicle objects in 2D and 3D time-resolved images.