Automated segmentation services
Our tooling has been developed for building powerful and custom AI models to reconstruct neurons, organelles and other features from biological microscopy data.
We offer a full service including training data generation and proof-reading in order to achieve high-quality results for your use cases.
● Neuron Segmentation● Axons & Dendrites Reconstruction● Synapse and Dendritic Spine Detection● Heuristical split and merge error handling● Annotation and proof-reading services available
Using our Voxelytics Connect tooling, we offer a repeatable, automated approach to circuit reconstruction and generating Connectome matrices from raw electron microscopy data.
We collaborate closely with your group in order to make the most out of your data. As part of a full service, we optionally generate the required training data and proof-read the results.
● Neuron reconstruction and synapse detection● Heuristics for split and merge error fixes● Annotation and proof-reading services available● Ready for 3D volume electron microscopy● (SBEM, Multi-SEM. FIB-SEM, TEM)● Fully integrated, collaborative workflow in WEBKNOSSOS
Blood Vessel and Nuclei Segmentation
Segment large biological features, such as blood vessels, nuclei or somata, for analysis or masking purposes.
● Blood Vessel, Somata, and Nuclei Segmentation● No training data required● Excellent for operations requiring masks
Custom AI Models
We are curious to learn about new use cases. Our tooling is flexible enough to be adapted to a wide range of image analysis tasks. Please get in touch to discuss your use cases and datasets with us.
● Segmentation, counting and measuring of objects● Support for many 2D and 3D image modalities (light and electron microscopy, ● Micro-CT, CT, MRI, Synchrotron X-Ray)● Custom trained for your use case● Scalable from gigabyte to petabyte-sized datasets
Raw image data from our collaboration partners
HPC and Cloud Ready
For our services, we either use cloud services or your Scientific Computing cluster. Our tooling is optimised for throughput of very large datasets and heavily makes use of parallel computing.
● HPC and Cloud Ready● Highly parallelised across manycore and GPU systems● Distributed computing with SLURM, PBS or other schedulers
Loomba et al. submitted a comparative study of neural structures in 8 Mouse, Macaque, and Human datasets (SBEM, each 0.5-2TB).
For that, a reliable, repeatable, highly-scalable solution for Connectome reconstruction across three different species with significant differences in cellular morphology was required.
The automated image alignment, neuron segmentation, and connectome reconstruction were carried out using Voxelytics.
Upload your data and define tasks
With your data on WEBKNOSSOS, we will schedule an intro call to discuss your research goals. Based on that, we will propose a project structure and estimate.
Work on your analysis project and have regular progress meetings(bi-weekly or monthly).We can optionally organise annotation or proof-reading of the work.
Receive the results
The intermediate results will be accessible on WEBKNOSSOS throughout the project.
You can then visualise the end results and receive them in a format of your choosing