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Voxelytics offers an end-to-end AI solution to process and analyze your large-scale microscopy data. Optimized for Connectomics.
Reliable and highly optimized workflows to align datasets, segment cells, predict synapses, reconstruct neurons, generate connectomes, and more.
Discover the possibilities of Voxelytics
Neuron reconstruction made by scalable minds with Voxelytics. Raw SBEM data by Motta et al., Science 2019.
Features
Automated microscopy data analysis
Voxelytics consists of powerful machine learning models built to reconstruct features from biological microscopy data.
Train and run the models needed for your analysis and execute tasks such as neuron segmentation, synapse detection, segmentation of organelles, and more.
Align and stitch EM datasets
Voxelytics supports volumetric imaging workflows from the beginning. Integrated routines for 3D alignment and in-plane stitching make it easy to turn a stack of individual image slices into a cohesive dataset for further analysis.
Dynamic mesh transformations and smart outlier detection enable smooth navigation through datasets.
Straightforward evaluation of results
Run your predictions on an evaluation box and compare the results with your ground truth.
Visualize and overlay your data in webKnossos to explore your reconstruction results.
Advanced Deep Learning for neuroscience
Benefit from our investments in tuned AI model architectures and augmentation pipelines. Combine multiple tasks, such as membrane segmentation, type detection, and metric learning, in a single model.
Easily use advanced features such as domain-adversarial training. Debug your models with rich evaluation and debug tools.
Seamless data visualization with webKnossos
Visualize your results with the webKnossos. Interactively combine raw microscopy data with the Voxelytics predictions and derive insights. Use the handy annotation features to label landmarks, adjust image fidelity and navigate through peta-scale datasets.
Generate training data for new or fine-tuned models. Manually refine your segmentations with the powerful annotation and proof-reading capabilities of webKnossos.
Full flexibility - without coding
Take advantage of the endless possibilities of Voxelytics. Mix and match (pre-trained) models and tasks to compose your own AI and reconstruction workflows.
Keep track of complex projects through the user-friendly interface and integrated results artifact management . Without a single line of code!
HPC and Cloud Ready
Voxelytics is designed for working with peta-scale datasets on cloud services or your scientific high-performance computing cluster (HPC). Our tooling is optimized for throughput of very large datasets and heavily makes use of parallel computing and GPU acceleration.
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Receive regular updates when we publish new features for webKnossos or share updates on the Voxelytics tools and services.
Dense neuron segmentation of mouse layer 4 somatosensory cortex
Full dense neuron instance segmentation using modified U-Nets and hierarchical agglomeration. Read blog article.
Nuclei detection
Execute the Voxelytics model for nuclei detection on EM data.
You will have your nuclei automatically segmented. Use the results such as the number of nuclei or their position to make meaningful scientific discoveries.
Custom models and analysis
Create your own custom workflows to analyze your microscopy images. Voxelytics supports many image 2D and 3D imaging modalities (light and electron microscopy, Micro/Nano-CT, CT, MRI) and can be adapted to a wide range of image analysis tasks.It is optimized to work with large-scale volumetric EM inputs.
Train your custom models and quickly iterate to reconstruct, count, and measure the size of objects.
References
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2021
Postnatal connectomic development of inhibition in mouse barrel cortex
Anjali Gour, Kevin M. Boergens, Natalie Heike, Yunfeng Hua, Philip Laserstein, Kun Song & Moritz Helmstaedter
Year
2021
Title
Postnatal connectomic development of inhibition in mouse barrel cortex
Authors
Anjali Gour, Kevin M. Boergens, Natalie Heike, Yunfeng Hua, Philip Laserstein, Kun Song & Moritz Helmstaedter
Publication / DOI
2021
Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy.
Carles Bosch, Tobias Ackels, Alexandra Pacureanu, Y Zhang, Christopher J. Peddie, Manuel Berning, Norman Rzepka, Marie-Christine Zdora, Isabell Whiteley, Malte Storm, Anne Bonnin, Christoph Rau, Troy Margrie, Lucy Collinson & Andreas T. Schaefer
Year
2021
Title
Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy.
Authors
Carles Bosch, Tobias Ackels, Alexandra Pacureanu, Y Zhang, Christopher J. Peddie, Manuel Berning, Norman Rzepka, Marie-Christine Zdora, Isabell Whiteley, Malte Storm, Anne Bonnin, Christoph Rau, Troy Margrie, Lucy Collinson & Andreas T. Schaefer
Publication / DOI