Imaris

Introduction
  • Imaris is a commercial software produced by Oxford Instruments.
  • It is specifically designed for 3D and 4D image analysis workflows and can efficiently process very large datasets (up to 100s of GBs) and can be used for batch analysis.
  • It is installed on all of the image analysis workstations in the facility.
  • The Imaris Viewer is a free image viewer you can download on your own computer (currently Mac and Windows only). With this you can explore your Imaris datasets including objects you’ve created, adjust display settings and take and export snapshots.
  • Since Imaris 9.3 was released in 2019, users of Imaris need to convert their files into .ims file format to use Imaris. See our facility resources below for some guidance about doing this

AIR Facility Licenses

• The various ‘floating’ Imaris licenses can be accessed from 6 workstations in the IGMM (five in CG.03 and one in S3.13 for IGMM South users).

• We have three “base” licenses with which you 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 anything else, you made need the use of an additional module.

• When you open Imaris, you should see this license selection window. Please tick only the licenses you need as otherwise you may be blocking other users from doing their analysis. We don’t currently have a way for users to book specific licenses.

Imaris license selection window

• The Imaris Modules section below is intended to help you understand which licenses you need and the information listed under facility resources are designed to help you use Imaris. If you are still unsure or would like some training, look here for details on how to access image analysis support.

• There is also a separate copy of Imaris without any additional modules on the computer that runs the Andor Dragonfly.

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. 

Facility Resources
  • A general guide to using Imaris as well as more specific protocols that we thought would be helpful for users can be found here.
  • We have also developed a range of videos for common applications in Imaris.
  • More general information on image analysis concepts and terms can be found here.
  • If you would like to know if there is a relevant workshop coming up soon please check here.
External resources

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