Tailored OEM Solutions from Imaris

Whether you are building a brand-new microscopy system or incorporating new functionality into your existing light-sheet or confocal microscope, our experienced staff have will help you add value to your project. If what you need is a fast 3D/4D visualization of terabyte sized microscopy images, accurate stitching of big microscopy tiles, GPU accelerated deconvolution or efficient file format for handling large images – we provide the solution.

Over the last 25 years, we have developed Imaris – a cutting edge software for 3D visualization and analysis of microscopy images. We can provide individual modules tailored to your existing acquisition or image analysis software.

3D Visualization for Confocal and Light Sheet Microscopy

In Imaris fast visualization of terabyte sized images is possible due to saving the image as a multiresolution pyramid. Imaris enables fast and smooth 3D visualization of images exceeding the computer RAM because it only renders the resolution matching the screen. This makes a decent experience for the human eye and ensures smooth rotations and zoom. Image on the screen is rendered as a mixture of two resolution levels and this mixture changes with the distance from the camera/human eye to the object.

The IMS file format stores a multi-resolution image pyramid in 3D block-wise layout using HDF5.
The renderer loads optimal image resolution levels to match screen resolution.
Data Caching on the GPU and in RAM improves performance significantly.
Data are stored in a lossless compressed format to save storage space.
Multi-threading of rendering and data decompression and upload facilitate interactivity.

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High Performance 3D File Format for Microscopy ImarisWriter

The open source ImarisWriter library is a high-performance file writer for microscopy images. It creates image files suitable for high performance visualization and analysis. The library takes care of all the details of multi-resolution resampling, chunking, compression, multi-threading and delivers its functionality to the user in a simple to use way.

ImarisWriter is free. Open source with an Apache 2.0 license
ImarisWriter is fast. A 100 GB image can be written in 1 minute
ImarisWriter is easy to use: Image data in. IMS file out
ImarisWriter works on Windows, Mac, and Linux”

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Stitching of big Microscopy Tiles for Light-Sheet and Confocal

Stitching of 3D microscopy tiles is an essential step when acquiring large samples with high resolution. Imaris Stitcher ensures fast alignment and stitching of big 3D microscopy tiles (tested up to terabytes).

Alignment and stitching of 2D, 3D or 4D overlapping image blocks
Alignment and stitching in XYZ
Possible alignment and stitching of multiple tiles with many channels*
Aligns and saves images up to Terabytes in size**
Alignment based on the image content in the overlapping regions
Corrects for camera vs microscope stage rotation. This systematic error of the acquisition can be estimated from just a few pairs of overlapping images which contain content and then used to reposition all images even if the signal is insufficient.

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Fast Deconvolution for Widefield and Confocal Microscopy

Imaris ClearView Deconvolution can be used to reduce noise, enhance contrast and sharpen the microscopy image.

Versatile - Optimized PSF for widefield, point scanning confocal and spinning disk confocal microscopy
Powerful – GPU-accelerated enhanced Richardson-Lucy and Inverse filtering algorithms
Accurate - Accelerated Gibson-Lanni algorithm for accurate PSF estimates, supporting spherical aberration correction in deep specimens
Extremely fast - Optimized CUDA workflow for scorching performance
Quantitative - “Energy conservation” matches total photon content of raw data and results
Innovative - Richardson-Lucy iteration acceleration with gradient-driven convergence in fewer cycles

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