Alignment services
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
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 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
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
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.
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.
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.