Frequently Asked Questions

Since Version 10.0

The graphics card and its driver are crucial for the stability and performance of Imaris.

Please check our System Requirements for supported graphics cards. And please update the driver regularly, at least every time you install a new Imaris version.

If you plan to work with large time series we recommend investing in more than 6 GB of graphics RAM. This will allow the graphics card to cache all textures for the display so you can browse much faster through the frames.

For deconvolution, GPU processing is supported on AMD and NVIDIA cards. NVIDIA is preferred because of better performance with CUDA.

Since Version 10.2

Imaris has been improved to run interactive on high resolution monitors. The interactivity may be compromised due to the higher rendering calculation requirement.

Up to Version 10.1

While you can run Imaris with high resolution monitor, the interactivity may be compromised due to the higher rendering calculation requirement.

Since Version 9.3

Imaris implemented GPU-accelerated calculation for the ClearView deconvolution function.

GPU processing is supported on both AMD and NVIDIA cards. NVIDIA is preferred because of better performance with CUDA.

The image size that Imaris can handle is not limited by RAM. If the data size/calculation requirement exceeds computer RAM, Imaris performs data caching to a hard drive.

However, data caching can slow down the processing speed. For better performance, we recommend having RAM at least twice the size of your image file.

The image size that Imaris Stitcher can handle is RAM limited. The minimum RAM requirement is around ten times the size of the largest volume overlap region. For additional Stitcher technical implementation details, please see here.

Since Version 9.3

Please check System Requirements for the latest information on hardware and operating systems.

As a rule of thumb the Minimum System works for datasets within 1GB, Recommended System for datasets up to ~5 GB, and High End System for dataset 10 GB or above. The requirement may vary depending on the file shape (i.e. long time lapse or large 3D volume) and the analysis workflow.

Please contact Imaris Support if you would like to discuss your specific need.

Since Version 10.1

Imaris is a multi-threaded application and many of the processing functions make effective use of multiple CPU cores. While we are working on optimizing algorithms to utilize the full power of multi-core systems with each new release, there remain some steps that are not yet fully multi-threaded. Thus, we recommend a balance between CPU speed and number of cores.

In general, we recommend fast (3.3 GHz+) CPUs with 16 cores (32 threads) or higher. Tested up to 32 cores (64 threads). Please check our System Requirements.

Since Versions 7.0 - 9.9

Imaris is a multi-threaded application and many of the processing functions make effective use of multiple CPU cores. While we are working on optimizing algorithms to utilize the full power of multi-core systems with each new release, there remain some steps that are not yet fully multi-threaded. Thus, we recommend a balance between CPU speed and number of cores.

In general, we recommend fast (3 GHz+) CPUs with eight cores (16 threads) or higher. Please check our System Requirements.

If your multi-core CPU is not running at 100% in Windows Task Manager, not all cores are used.

It may be due to (1) the calculation is not fully multi-threaded, or (2) Imaris may need to load image data from the disk into RAM for processing. In general, disk access in Imaris will only use one thread per disk.

Since Version 9.3

If you are using Windows 10 Build 1903 and newer, you can use Imaris in Windows Remote Desktop session (RDP) assuming you have a dedicated 3D NVIDIA or AMD card.

For earlier Windows 10 build (180x and earlier) or Windows 7/8 or 8.1 the only way to get Imaris working in RDP sessions is to use an NVIDIA Quadro M-Series or newer (e.g., M4000, P4000). The Quadro card driver supports OpenGL independent of the Windows version.

There are other remote desktop solutions (TeamViewer, Anydesk, etc.) that do not rely on OpenGL and may work for your system.

Please consult your IT department before installing remote desktop solutions as there might be network restrictions in place.

The IMS file format is based on the Hierarchical Data Format (HDF5) that is designed to work with huge multidimensional data and is optimized to allow extremely fast visualization of huge volume data. To facilitate this, the format stores not only the original image data but also lower resolution versions of the original data.

For additional information, please see here.

Yes! ImarisWriter allows you to quickly write image files suitable for high performance visualization and analysis in the Imaris5 File Format.

Since Version 9.3

Imaris can export Surfaces in the *.wrl and *.iv formats (by 3D View > Export Selected Objects. These formats are compatible with MeshLab and other 3D animation softwares. This short tutorial shows the export and import steps of wireframe models.

Since Version 9.3 

When converting an image file into the IMS format either in Imaris Arena or by the ImarisFileConverter, new IMS file is generated with the same name as the original image file without modifying or deleting original image file.

If both files exist in the same folder, then only the IMS file will appear in the Arena view.

In most cases you will be able to read IMS files written by older Imaris versions into later ones. There are some limits:

• IMS files version 3.0 (written, e.g., by Imaris 3.0 to 4.5) cannot be opened directly in Imaris 9.5 or later. Workaround:
  • remove the. ims extension
  • observe the folder in Arena
  • double-click the file to convert it to ims5
• Surfaces written in versions before 9.0 can be opened in newer versions, but with reduced functionality. Workaround: In case you have not done any manual editing, use Surfaces > Creation tab > Recompute to recreate them in the new format.

IMS files written in newer software versions may not be read in earlier Imaris versions. When you have problems, you might have partial success by using ‘Save As’ or ‘Export’ where you can choose an older file format in the ‘Save as type’ field in the newer version. It is likely that not all parts of the Imaris scene will be saved in the older format.

Since Version 9.3

Imaris supports file conversion from most proprietary files from major microscopy vendors. The complete list of files that can be directly converted is located at: Help > Reference Manual > Supported File Formats.

To open an image file in Imaris it first needs to be converted into the IMS format using the Imaris File Converter or within Imaris Arena.

Since Version 9.9

Yes, Imaris supports direct import of segmentation results (of H5 or Tiff labelled images) into Imaris surfaces. For example, you can export the segmentation results from the open-source pixel classification algorithms in ilastik or Labkit and import them into Imaris as surfaces, Imaris can also load spots and tracks created in MaMuT or TrackMate.

Since Version 8.4

In Imaris open File > Preferences > Creation Parameter. Select the creation parameter you want to save, use the export button, and save them to the specified location.

Since Version 8.4

In Imaris open File > Preferences > Creation Parameter. Use the ‘Import’ Button and browse to the stored creation parameter. In the corresponding object creation wizard, you can select the imported creation parameter via the Drop-Down menu.

There are several ways of importing data into Imaris. In this video you will find shortened instructions. The detailed version of the video, covering some additional issues, such as: Arena, Imaris File Converter and BioFormats can be found here.

Since Version 10.1

Imaris 10.1 brings native machine learning segmentation to Imaris, where you can train the AI pixel classifier to segment the image by simply painting some foreground pixels and some background pixels and letting the machine learning system infer the rules that fit your painting. This is a very intuitive and easy way to set up segmentation that is significantly more versatile than a simple threshold. For additional information, please see Imaris 10.1 release notes, AI trainable segmentation webinar and this training tips tutorial.

Since Version 10.0

In Imaris 10.0 Filament Tracer, the proven autopath method for tree-like structures, is enhanced with machine learning (multi-scale) seed points and segments classification for more versatile, accurate and repeatable detection. For further information, please see Imaris 10 release notes, AI powered Filament Tracer release webinar, and this detailed Filament Tracer tutorial.

Since Version 9.6

Imaris allows you to classify objects by machine learning that utilizes all standard statistics calculated by Imaris and additional ‘machine learning statistics,’ that provide more information about the local intensity landscape. For additional tutorials and application examples, please see the Imaris 9.6 release notes and this Home School recording.

Three things to consider when deciding which object works the best for your analysis:

• The object shape – Can it be approximated by a sphere? Is it better modelled by filament?
• Desired statistical output
• Dataset size/complexity – If processing speed is a concern, stay with simpler models

For additional details, please watch this Home School recording that provides an overview of all Imaris objects.

Since Version 7.0 

(1) Go to File > Preferences > Statistics, and check if specific statistical values are selected.

(2) Go to the Statistics tab under the component of interest, select the statistic value, and click ‘Export Statistics on Tab Display to File.’ Alternatively, you can export all available statistics by clicking ‘Export All Statistics to File.’

(3) Statistics can also be saved from Vantage for the values used for plotting.

Since Version 7.6

This tutorial walks you through the process of creating a custom-shaped region in your 2D or 3D image.

For more in-depth discussion on the Surface Contour topic, please watch this Home School recording.

Since Version 7.6

Follow this tutorial to learn how to precisely position the vertices of contour lines, how to edit only a few vertices of an otherwise complete contour, and how to translate, rotate, and scale contour lines.

Since Version 5.7

Filter offers a quick and easy way to find objects with certain statistical values. The selected objects can be labelled, duplicated, or removed for various application needs.

This tutorial shows you the various ways to use the Filter tool.

Since Version 9.3

If you run Batch analysis, the aggregated statistics results can be accessed from Arena > Folder Batch History > Export Statistics to csv file.

If you have manually segmented several images, or segmented them automatically one-by-one, it is still possible to aggregate the statistics from several different images into a single .xls/.csv/.xml by following these steps.

Since Version 8.0

(1) After creating an object, go back to the Creation tab

(2) Click ‘Store Parameters for Batch...,’ check Store Location ‘Favorite Creation Parameters’

(3) Go to File > Preferences > Creation Parameters, click ‘Export...’, share the saved *.icpx file

(4) *.icpx file can be imported to other computers with Imaris by File > Preferences > Creation Parameters > Import...

Imaris provides many tools to study colocalization. Depending on the signal characteristics you can choose to use either intensity-based colocalizations tools to quantify diffuse signals or object-based colocalization tools for structures that can be represented as objects.

This short tutorial video shows the comparison between intensity and object-based colocalization. For more in-depth tutorials and application examples, please see here.

Since Version 9.3

• In the file system, create folders for the different groups of datasets
• Move or copy the datasets into the folders
• In the parent folder, create a new Batch Pipeline
• Right click on the Batch Pipeline and select ‘Run Batch including Subfolders’
• After processing is finished select the folders with the processed datasets
• Click ‘New Plot’

For more details on Vantage plot comparison, please see this Imaris HomeSchool recording.

Since Version 9.3

• Make sure the objects in the 3D View Scene tree of each dataset have a name that reflects the group they belong to. For example:
• ‘Surface 1 Group A’ would be the identical name for Surfaces which need to be sorted in Group A
• ‘Surface 1 Group B’ would be the identical name for Surfaces which need to be sorted in Group B



• In Arena select all datasets by pressing CTRL-A and mouse select (*All datasets of all groups must be in the same folder!)
• Click ‘New Plot’ to show the result

Results:

For more details on Vantage plot comparison, please see this Imaris HomeSchool recording.

Since Version 10.1

Starting with version 10.1 Imaris opens 2D images in a 2D mode and the statistical values are computed specifically for 2D images. Furthermore, statistics and features that do not make sense in 2D have been removed in this mode, and some additional variables have been included such as Circularity and Ellipse Axis Length.

Since Versions 5.7 - 10

2D datasets are handled like 3D datasets, so you get the same statistics but be aware of the interpretation of these values:

Area

The area statistic refers to 3D surface area even for a 2D dataset. Imaris creates a surface around the voxels, including the top, bottom, and side. The reported area will consider all these faces of the surface.

Instead, please use 'Number of Voxels' and multiply it by the XY size of a pixel to get the 2D area value.

Volume

Imaris computes a 3D Volume which takes the Z voxel size into account as given at 'Surpass - Edit - Image Properties - Geometry - Voxel Size - Z'.

If you set Z voxel size = 1, this value will reflect the 2D area. *There may be a rounding error for very small Surface objects.

• Add the object you want to detect (e.g. Surfaces)
• Follow the wizard to optimize the parameter and detect the objects you are interested in
• Once the wizard is finished, open the Creation tab:

In this Creation tab you have several choices.

• Re-Enter the detection or classification at the corresponding step of the wizard to slightly adjust the parameter used
• Store the parameter used to reuse them on other images
• Review the parameter used/listed

Re-Enter the detection or classification at the corresponding step in the wizard to slightly adjust the parameter used

You can re-enter the detection at different steps:

• Surfaces starts the detection at the first step in the wizard
• Surfaces from Seed points starts in the Seed point detection step in the wizard
• Classification starts in the classification step in the wizard

Store the parameter used to reuse them on other images

In the Creation tab click on ‘Store the parameters for batch’.

Provide a name and enable the Store Location

a) Arena:

• this shows the parameters in the Arena in the folder of the image
• if you expand the section ‘Command Create Surface’ you can see the details about the parameters used
• to reuse this in a batch mode you need the corresponding Batch module license



• Right click to the creation parameter gives you the choice to apply the parameter to the images listed in the corresponding folder or to apply them to all the images listed including the subfolders



• Without a valid Batch license, you see the following:



• Reveal in Finder/Show in Explorer enables you to e.g. copy the creation parameter to another Imaris machine or to share the parameters used with colleagues/collaborators

b) Favorite Creation Parameter:

• The Favorite Creation Parameter can be found in Imaris – Preferences – Creation Parameter. Here the existing parameters are listed, can be reviewed, exported or imported



• To reuse the same parameters, add a new surface object and select the corresponding favorite creation parameter in the drop down list



• Go through the wizard with the exact same parameters or slightly adjust them to improve the detection result on the corresponding image

Review the parameter used/listed

All used parameters are listed, and the section marked with ‘[]’ define the corresponding step in the wizard:

Since Version 9.3

Texture cache affects rendering responsiveness. The default value is the physical RAM of your graphics card, and it should work well most of the time. For graphics card with large RAM (>16GB), reducing this value to 12-16GB may sometimes increase responsiveness.

You can adjust the texture cache used by Imaris from File > Preferences > Display.

You can adjust RAM used by Imaris from File > Preferences > Calculation.

The default value is set at half of the system RAM. When modifying this value, please make sure the system has sufficient RAM to run the machine. If you have 128 GB RAM, set this value at 100 GB or lower to ensure system stability.

You can change data cache location from File > Preferences > Calculation.

The default location is usually set to the C drive. If you have multiple hard drives, we recommend setting the data cache location to the faster drive (PCIe SSD) and to avoid using the system drive as a cache drive.

Imaris can write in parallel to different paths if more than one path is added. Please be aware that if multiple drives are used as a cache drive, the one with fewer free space will limit the usable space on the others as well.

If you are an administrator, you can force some settings to apply to all users from File > Preferences > Imaris Administrator > System Preferences. Remove the check mark 'Is editable by Users' to enforce it on all current and new users.

Settings that can be set system-wide include number of threads, texture cache, RAM limit, data cache paths.

Please refer to ImarisXT section.

Before reseting the Preferences please check if there are Creation Parameter stored and export them before continuing. See the How can I export Creation Parameter section.

To reset user settings:

(1) Open Imaris, make sure only one instance is running

(2) File > Preferences > Reset Preferences…

(3) Restart Imaris

Note that some settings are only accessible from Registry. We do not recommend that users edit the registry in most cases. If you need assistance, please contact your regional Support Team.