Dataset alignment

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

Alignment services

After
Before

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.

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

Raw image acquisition by Francis Crick Institute

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

After
Before

Raw image acquisition by Carles Bosch, Francis Crick Institute

After
Before

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 normalisation and gradient correction in large-scale datasets. 
● Histogram-based correction of tiles or sections● 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.
● Stitch 3D volumes from Micro-CT or Synchrotron X-Ray sources● Seamless border blending

Illustration

Raw image data by Carles Bosch, Francis Crick Institute

Benefits

Battle-Tested

Proven results for many large-scale EM datasets. Optimised 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.

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.

How does it work

1

Upload your data and define tasks

First, let's schedule an intro call, have a look at your data and discuss your project's needs. Based on that, we will propose a project structure and estimate.

2

View the results in webKnossos

Have a look at the results on webKnossos. Thanks to the fast browsing, you will be able to fly smoothly around your aligned data.

3

Receive the results in a format of your choice

You can now continue working with your data on webKnossos or receive the results in a format of your choice.

Pricing

Image alignment and pre-processing services to get your analysis started.

Please contact us if you are interested in 3D Stitching or custom pre-processing services, or any of the use cases described above.

Pricing range:3D Alignment from €5,000 per dataset, excl. VAT.2D Stitching from €5,000 per dataset, excl. VAT.

Fill out the form to have a call with us about your project!


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