The MCF offers a powerful full imaging software package known as Imaris (v8.4) provided by Bitplane, Corp. This package gives the user, as a small sample of its capabilities, the ability to view their confocal images in 3D mode, make short movie clips of their 3D images, trace filaments in tissue samples, and form and view cells and tissues with added surfaces. It also gives detailed statistical data of the processed scanned samples. The software is installed on a stand-alone computer workstation and is available on a first-come first-served basis, and is free to use. Email or call the core manager for access to the computer room.
Imaris 8.4 Modules That We Have:
Imaris Bitplane’s core software module delivering basic functionality.
ImarisCell: Specifically designed for the analysis of 2D, 3D, and 4D cell images.
ImarisLineage: Enables the study of cell lineages, including cell division detection.
ImarisColoc: Powerful colocalization analysis for multiple bio components.
ImarisXT: Two-way interface from Imaris to classic programming languages.
ImarisVantage: Extract more from your data, and visualize your cells in 4D.
MeasurementPro: Extract critical statistical parameters from your microscopy images.
ImarisTrack: The most powerful live cell imaging software for tracking and analysis.
FilamentTracer: The intelligent way to visualize and measure filamentous structures.
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.
- 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
- Automatically works on 2D, 3D or 4D datasets
ImarisLineage is the new module which builds on the functionality of the powerful and widely used ImarisTrack. ImarisLineage provides tools for accurate automated or manual tracking of dividing cells in 2D/3D time series. 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 new 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
Obtaining accurate information about the position of stained tissue and cellular components is the primary goal of digital microscopy. ImarisColoc has been designed to give researchers the most powerful colocalization analysis tool to quantify and document co-distribution of multiple stained biological components.
- 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
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
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.
- Dissect multi-dimensional, multi-object images imags
- Visualize your image data in 5 dimensions
- Create fast, explorative and interactive multi-dimensional plots
- Create side by side ready to publish one dimensional plots to compare groups
- Export figures and annotations into your presentations
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.
- Obtain, view and export statistics
- Obtain precise measurements of intensity values
- Select objects of interest for extracting parameters
- Sort and classify objects in real-time based on parameters
- Measure distances between points within an object
ImarisTrack is the most powerful commercially available live cell imaging, tracking & analysis software that rises to the challenge of monitoring temporal changes in biological systems (2D and 3D images over time). ImarisTrack is based on a choice of multiple sophisticated manual and automatic tracking algorithms and also includes an intuitive and interactive track editing tool if manual correction is necessary.
- Automatically track objects in 3D + time
- Choose from a large variety of tracking algorithms
- Handle thousands of objects and time points
- Manually edit, create or revise tracks
- Generate object and track statistics based on changes
FilamentTracer is the most advanced software product for the automatic detection of neurons (dendritic trees, axons and spines), microtubules, and other filament-like structures in 2D, 3D and 4D. When combined with ImarisTrack, detection of temporal changes in length and volume of developing spines and dendrites will help researchers understand alterations caused by developmental and environmental changes.
- Versatile tracing methods
- Obtain branch length and diameter statistics
- Manually draw segments with automatic centering
- Utilize multiple branch selection methods
- Visualize filaments along with non-filamentous structures
ImarisBatch is an Imaris subsystem for the processing of 2D, 3D, and 4D image series in batch. This subsystem saves valuable time when running repetitive jobs because processing can be queued and completed without interaction from the user. Since the introduction of Imaris 8.0 batch operations can be triggered directly from the Arena view. The user can execute a pre-defined image analysis protocol on all images of one group or all images from multiple groups. The results of batch analysis can be directly displayed and explored in Imaris Surpass or Imaris Vantage.
- Save valuable time by batch processing
- Reproduce exact analytical procedures
- Decouple time consuming procedures from interactive sessions
- Batch process the full experiment and get the results which preserve the experiment structure
- Utilize large servers for parallel processing
Imaris Protocols and Tutorials:
The Imaris Learning Centerhosts 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 from the Imaris web site, specific for the software version 8, which may help you in navigating through the many intricacies of the complete software package. The Imaris web site not only provides the limited number of links listed below, but also provides links to many other topics of interest including many of the company’s recent upgrades of the Imaris software capabilities.
Below is to a tutorial/movie prepared by a departmental student as part of their respective laboratory’s research interests. This tutorial primarily uses the Cell Module of the Imaris program and shows how a user can add and remove volume to a cell body and then manipulate that built-up image to obtain the analysis desired. Although the video is specific for that laboratory’s research work, there may be beneficial information included that would help others to understand the work flow of the Imaris program: (please turn up the volume of your speakers for this tutorial):
Below are the Quick Start Tutorials guide, and the Imaris Reference Manual (for version
7.3.1) of the Imaris software. Although this version of the Reference Manual was
written for an earlier version of the software, users may glean information from the
manual that would be of benefit to their journey through the use of our version of
the Imaris program (the manual for version 8.4 is forthcoming):