Voxelytics Align

Full service for pre-processing large-scale 2D and 3D microscopy datasets.Robust Alignment, Registration, Stitching, Gradient Correction and Normalization.

Use Cases

After
Before

Raw image acquisition by Francis Crick Institute

3D Alignment and Registration

Proper alignment of 3D electron microscopy image stacks is crucial for effective manual and automatic analysis. Overlapping regions are stitched together into a coherent dataset.
We offer a full service for the alignment of 3D electron microscopy datasets. Just upload the dataset and receive the results. No coding required.

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    Dynamic mesh transformations for fine alignments
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    Support for arbitrary shapes through masking
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    Efficient global alignment with RANSAC
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    Robust outlier (e.g. debris or artifacts) detection

2D In-Plane Stitching and Montages

Easily combine individual image tiles produced by your microscope into a single plane. Overlapping regions are stitched together with smart outlier rejection.
We offer a full service for the alignment of large-scale 2D electron microscopy or other images. Just upload the dataset and receive the results. No coding required.

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    Dynamic mesh transformation for fine alignment
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    Support for arbitrary shapes through masking
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    Efficient alignment with RANSAC


Raw image acquisition by Carles Bosch, Francis Crick Institute

Raw image acquisition by Max Planck Institute for Brain Research

Normalization and Gradient Correction

Due to the sensitive nature of image acquisition, some artifacts are inevitable. Sections may show uneven brightness and contrast. There may be gradients across tiles or throughout the dataset.
Fortunately, these artifacts can be corrected using our technology. As part of our alignment and stitching services or separately, we offer services for normalization and gradient correction in large-scale datasets.

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    Histogram-based correction of tiles or sections
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    Gradient correction within a tile or across the stack

Stitching of 3D Tiles

Imaging large volumes with Micro-CT or Synchrotron X-Ray Tomography requires sub-dividing the volume into 3D tiles.
We offer services for stitching reconstructed tomography tiles into a coherent dataset.

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    Stitch 3D volumes from Micro-CT or Synchrotron X-Ray sources
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    Seamless border blending
Illustration

Raw image data by Carles Bosch, Francis Crick Institute

Built for Life and Material Sciences

Benefits


Battle-Tested

Proven results for many large-scale EM datasets. Optimized for SBEM and serial-section SEM or TEM.

Fast Turnaround Times

Depending on the characteristics of your dataset, we are able to deliver results within days. More challenging datasets require a few weeks.

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Delivery through webKnossos

Browse and analyse your pre-processed datasets immediately in webKnossos or export in a common data format.

Continuous Improvements

With every processed dataset, we improve our tooling to deliver even better results.

Pricing

Our image alignment and pre-processing services get you started with data analysis.


Please contact us if you are interested in 3D Stitching or custom pre-processing services.

3D Alignment

From €5,000

per dataset, excl. VAT

Fully managed service

Includes Alignment, Normalization and Gradient Correction

Run in the cloud or on your HPC cluster

2D Stitching

From €300

per dataset, excl. VAT

Fully managed service

Includes Alignment, Normalization
and Gradient Correction

Run in the cloud or on your HPC cluster

  • Quantum CEO & our partners
  • Quantum CEO & our partners
  • Quantum CEO & our partners
  • Quantum CEO & our partners

Looking for Automated AI Image Segmentation?

Alignment, stitching, and normalization are typically only the first steps for reconstructing microscopy datasets.
With Voxelytics Connect we offer a fully optimized machine learning solution for image segmentation for neurons and synapse detection.