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Imaris 

Imaris (Bitplane, Inc) can be used for segmentation, visualisation and analysis of 3D and 4D (3D + time)  imaging data. It can read most imaging files formats, including .ims, .nd2, .tif, and .lif.

Advantages

  • High-quality rendering and segmentation of 3D and 4D datasets.
  • Functionality can be extended via compatibility with ImageJ/Fiji macros and MATLAB scripts.

Disadvantages

  • Commercial software/ requires a license.
  • Can be slow for working with files on remote share locations (such as folders on the Datastore). This can sometimes necessitate moving data to a local hard drive.

Availability in AIR

  • The IGMM Advanced Imaging Resource holds three licenses of Imaris 8.4 (with version 9 coming in July 2017). It can be used on any of the Windows imaging analysis workstations (Cleopatra, Holycow and Holybones).
  • With any of the three licenses you can perform a number of things including creating “Surfaces” and “Spots”, carrying out co-localisation analysis, setting up comparisons between groups in “Arena” and exploring the resultant data with the graphing options in “Vantage”.
  • For further features you may need to use one of the additional modules. The facility has 2 copies of each of the Track, Lineage and Batch modules and 1 copy of each of the Cell, XTensions and Filament Tracer modules. Details of these modules can be found below. 
  • When using Imaris in the facility, you need to book the workstation, an Imaris base license and licenses for any additional modules you want to use. The licenses can be booked via the "Imaris licenses" page on the facility booking system.
  • There is also a separate copy of Imaris without any additional modules on the computer that runs the Andor Dragonfly. With this copy you can visualise your data and export them as movies or snapshots to show at lab meetings, etc.

Imaris MOdules

    - Track

    This module is needed to track objects over time in 2D or 3D time-lapse datasets.  The location of objects can be tracked over time, as can other features, such as their morphology, intensity, and speed.

    - Lineage

    This module is for tracking dividing cells and will create lineage tree of division events from each cell through a time-lapse data set. A number of statistical measures are calculated, such as generation number, cell cycle duration, and time since first or previous division. 

    - Batch

    This can be used to apply the same analysis parameters to your whole dataset. 

    - Cell

    This module is designed for analysis of detected cells; it can associate multiple cellular components across your dataset. It can give outputs like nucleus to cytoplasm ratio or number of vesicles per cell.

    - XTensions

    A programming interface between Imaris and other programs. It be used to link Imaris to ImageJ/FIJI as well as Matlab and Python scripts. Bitplane host a forum where people share XTensions with each other. 

    - Filament Tracer

    Designed to measure filamentous structures. Originally developed for analysis of neurons it can be used to carry out sholl analysis and analysis of dendritic spines but it has also been used for blood vasculature and cytosketeletal filaments. 

    Additional information

    • Product page for Imaris 
    • Scene Viewer - free offline viewing software. To download this you need to scroll down to the bottom of the linked page where you can register to be sent a download link.
    • Watch this space for user guides for oft-performed analysis but in the meantime the learning page provided by Imaris also has a number of helpful videos.