Imaris Information

 Imaris is used for visualization and analysis of multi-dimensional microscopy data,

Imaris Stitcher is an independent application for aligning and stitching multiple FOVs (see below).

You can use Imaris on your own computer or on one of the Image Analysis workstations at Ullmann building, room 028.

We currently have 5 Imaris floating licenses available for usage anywhere inside WIS campus, and 1 Imaris Stitcher floating license 

Imaris is Fully supported, If you encounter problems you can contact Ofra Golani or email directly to Imaris support ( .

In your email please state clearly that you work at Weizmann Institute and please cc Ofra Golani on the email.  

Latest version 9.9.1 


Imaris usage must be scheduled through Internal Services=>Advanced Light Microscopy (as well as the the image analysis workstations)

If you are not authorized or need user account, please contact Ofra Golani or Vitaly Golodnitsky

You should send the following information to Ofra Golani :

  1. The name of the computer you use for Imaris 

  2. The userid you use on that computer

  3. Your name + PI Name 

  4. Telephone number you can be reached on

When you start Imaris a new window will popup asking if you want to use Imaris Cell and/or Imaris Batch

If you don't need these modules or don't know what they are - simply leave them unchecked and click OK. Most people don't use them

Learning Material

Look at Imaris Help for Quick Start Tutorials

Video Tutorials can be found in Imaris Learning Center.  Start with watching one of the Introductory video tutorials 

Hands-On material for self learning of Imaris from a course conducted in July 2021 using Imaris 9.7.2 is available upon request.

Older versions used in our Image Analysis course can be downloaded here.

Installation Instructions

  1. Login as administrator

  2. Download the installation files, from the Imaris 9.9.1 Installation Files  

  3. Start the setup program suitable for your OS (.exe for Windows, .dmg for Mac) and follow the instructions.

  4. During installation: If you have used Imaris before with Arena - select to install also Imaris Arena Migrator.

  5. If this is the first time you install Imaris you need also to install  the compiled Matlab file which enables using Imaris extensions (MCR_Runtime_R2020b... for Imaris 9.7+, or MCR_Runtime_R2020a... for Imaris 9.6 or Mac) .

  6. You need also to install ImarisConvertBioformats_Latest.exe file

  7. You can choose now if you want to install Arena, which is useful for batch analysis. If you do please follow also Data Storage Path Specification below

  8. Start Imaris

  9. The License Settings Dialogue will appear
    License installation

    Configurator con

    - start the 'Imaris Administrator' by clicking on the Configurator icon

    - In the new window select 'Add License Location'
    - Now choose 'Define Floating License Server' and specify the server name (microarray2) or the server IP-Address ( and the port. (Default port is 2700).

  10. Hit 'OK' than 'Finish' and finally 'Start'. Imaris should then start.


Imaris Viewer

Allows 3D visualization (no analysis) and does not require any license.  

Imaris File Converter

 You can use Imaris File Converter  to convert your data from your native microscope format into Imaris format in the background without using Imaris license. 

It is installed automatically when you install Imaris or Imaris Stitcher.

Imaris Converter does not require a license, and scheduling through internal services.

At the first time you run the File Converter, you need to activate the Bioformats plugin (after running ImarisConvertBioformats_Latest.exe file) :

  • Click on the orange “Download ImarisConvert-Bioformats Plugin” icon

  • Then click on the Blue “Detect Installed ImarisConvertBioformats” icon:

  • and Click OK to activate it.

Imaris Stitcher

 You can install and use Imaris Stitcher to align and stitch together multiple fields of view.  

The Installation file is in the same Installation folder.

More info is available online, or see our Imaris Stitcher User Guide.  

We have one license of Imaris Stitcher, and you need to schedule its usage through Internal Services=>Advanced Light Microscopy.


Optimize your Imaris Preferences

It is recommended to make sure that Imaris recognize well your computer resources, to point to cache disk space, and to select the only the desired Statistics:


Go to File > Preferences

System: If you have a graphic card: make sure that Imaris recognize it correctly (Graphics items)

Display: make sure that Imaris recognize well the amount of graphic card memory (Texture cache Limit)


A rule of thumb is that Imaris require 5-10 times of your data set to work properly

  • Make sure that Imaris recognize well the number of available cores (Number of Parallel Jobs)

  • Set the available RAM to be about 50%-90% of your computer RAM (Memory Limit)

  • Set Cache File Path to a disk with enough free disk space . If you have a fast drive (SSD) with available disk space point to that drive


Limiting the calculated statistics can save a lot of time.

You can limit them to minimal (eg volume, center) when you tune the segmentation parameters and activate them again when segmentation is complete.

In the Preferences > Statistics you can activate / deactivate the statistics measurements of each module (Cells/ Filaments / Spots / Surfaces)

You can also access Statistics Settings from the toolbox icon in the statistics Tab.


Migrate old Arena files - from Imaris versions older than 9.2

Your own computer – single user

Use ImarisArenaMigrator to export old data saved in Arena. Follow this movie for instructions. 

On the first run it suggest to open the Arena migrator automatically, otherwise you can find it under

Shared workstation at your lab

Each user should migrate his/her own Arena

See instructions above (in Your own computer section)

If you have users who left the labs and you want to migrate their old files, please contact us directly for help.