arivis Scientific Image Analysis

Artificial Intelligence, Machine Learning and Deep Learning

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Boost Your Research with Advanced AI Methods

AI, Machine Learning and Deep Learning Tools

With Machine Learning and Deep Learning tools available in the ZEISS arivis scientific image analysis eco-system, segmentation of multi-channel images becomes quick and easy. 

Your scientific expertise is enough to mark and classify structures of interest in your samples. Let The AI toolkit in the cloud train your neural network, then export your AI-trained model. Use the model to set up an end-to-end pipeline with a few clicks.
With arivis machine learning and deep learning tools,  you get reliable results in hours instead of weeks or months.

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  • Easy to use, guided workflow for users with little image analysis knowledge 
  • Labelling a few lines in the image is enough to define expected results
  • Robust, reproducible, and reliable analysis results 
  • Save time by re-using training data on various data sets
  • Full integration with open platforms and various standards
  • Previews of results and probability maps provide fast, direct feedback
  • Automated segmentation and analysis for possibilities beyond manual methods
  • When other algorithms fail or are tedious, experts may want to try arivis

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Why use Machine Learning Algorithms

When an imaging specialist designed a  conventional algorithm it answers one specific question. A Machine Learning algorithm can be adapted to various questions by training it. The Machine Learning algorithm “learns” patterns and adapts itself.

The researcher need only annotate regions of interest in a small part of the image to train the model. By learning patterns, Machine Learning and Deep Learning tools learn to classify samples, and this information can be then used to identify structures in the entire image and also in other images.

apply Applicable Applicable to any image of any size and number of dimensions
settings-configuration Easy to Use A user-friendly guided workflow, no coding required
reload Fast Feedback Fast feedback during training with result previews
chart-statistics-key-figures Easily Scalable Batch analysis compatible,  easy image analysis scalability

Machine Learning Workflow

Our Machine Learning  workflow is easy to use and guides you through three simple steps.

Train Use specific user knowledge to define ground truth and train the algorithm to recognize and classify structures of interest.
Save Save and download your trained model for offline image analysis. You can improve it by adding more labels or reuse it on new images.
Apply Click to start segmentation,  or use the Batch Analysis Module to process hundreds of data sets simultaneously.

Deep Learning Workflow

Multiple ways to use your AI-trained model

Learn about multiple ways to use your AI-trained model.

Hardware and Data Agnostic ZEISS arivis scientific image analysis eco-system supports a wide variety of multidimensional image file formats and imaging hardware sources. Never  worry about compatibility again!
Train a Model with a Few clicks Train your deep learning model using the arivis AI toolkit on ZEISS arivis Cloud. The process is intuitive and requires only partial annotations, saving considerable time. Tweak it as needed.
Automated End-to-End Pipelines Your neuronal network is easily imported into and used with ZEISS arivis Pro, ZEN or well-established open-source analysis platforms. Let the software work for you. Get reliable results within hours.

Why use ZEISS arivis Cloud

Our Deep Learning workflow allows for reproducible results and enhanced throughput.

academy-campus Deep Learning Made Accessible The user-friendly interface enables researchers to easily train an advanced AI-driven model with no need to code.
time-period Added Value and Faster Results Invest on what really counts - your research and accelerated commercialization. Save on workstations and computation resources.
group-workshops Expert and Peer Support Our community is your first point of contact. Our experts will be happy to assist you to resolve image analysis challenges.

Machine Learning Workflow


Deep Learning Workflow with arivis AI toolkit on ZEISS arivis Cloud and ZEN Intellesis

This tutorial demonstrates how to use the arivis AI toolkit on ZEISS arivis Cloud (formerly APEER), with ZEN Intellesis and ZEISS arivis Pro (formerly Vision4D) for deep learning applications. ZEISS arivis product family supports the Open Neural Network Exchange (ONNX) and the ZEISS CZ models. ZEISS arivis Cloud enables easy model annotation and training without programming knowledge. You can create new models or combine existing ones into customized workflows. It is easy to set up end-to-end automated image analysis pipelines with ZEISS arivis Pro, based on the imported fully trained neural networks from various libraries and backends.


Annotate for automated Deep Learning-driven image segmentation

Hippocampus tissue section, transmission electron microscopy. 30 TEM sections with 309 mitochondria were manually annotated using ZEISS arivis Pro (formerly Vision4D, ver. 3.6). This manual annotation was used to train an ONNX U-Net model for automated segmentation, which was applied to the entire dataset. The mean intensity to volume ratio was then calculated to show differences in mitochondria phenotype. The results were shown as color-coded object classifications. The imaging data was kindly provided by Dr. Wendy Bautista, MD Ph.D., Barrow Neurological Institute, Phoenix Children’s Hospital. 

Full integration in ZEISS arivis 

Machine Learning and Deep Learning tools are fully integrated into the ZEISS arivis product line allowing researchers to combine segmentation results with other pipeline functionalities.

These include:

  • Filtering (e.g. on volumes, intensities, etc.)
  • Tracking
  • Grouping
  • Distance measurements
  • Probability map used as a basis for a subsequent segmentation 
  • Integrated workflow with various options for connected software and training platforms

arivis Machine Learning and Deep Learning tools work for several different multi-dimensional images from many microscopy modalities:

  • Fluorescence Microscopy
  • Superresolution Microscopy
  • Transmission Light or Label Free Microscopy
  • Confocal Microscopy
  • Light Sheet Microscopy
  • Electron Microscopy (2D and 3D)
  • X-ray Microscopy
  • CT and MRT images

All image formats are supported by ZEISS arivis will also be compatible with our AI functionalities. CZI, TIFF, JPG, PNG, TXM and all Bio-Formats compatible images.


The arivis Image Analysis Platform

The arivis Scientific Image Analysis Platform is a flexible computing universe that scales, parallelizes, and streamlines all imaging workflows. With arivis' easy sharing functions your organization can enjoy data proficiency and efficiency at new levels. arivis includes integrated toolsets that handle everything, from file storage format to project and user-specific computations, to reporting. The platform's hubs connect datasets and manage central imaging databases and raw data exposure, while also enabling Machine Learning and AI routines.

placeholder40px ZEISS arivis Hub A nucleus of computational activity and collaboration at scale. ZEISS arivis Hub enables design and execution of large-scale experiments that produce results from images, whether datasets are already stored or are actively being produced. Mass quantities of microscopy data are onboarded and processed by a virtual team of computational workers. Smartly utilize processing cores in servers or workstations with maximum possible speed.  
placeholder40px ZEISS arivis Pro

Extract results from your scientific images with ZEISS arivis Pro. Make the most of hardware power adjustments and smooth interactivity on microscopy datasets of virtually unlimited size. The software unites multiple tools for visualization and advanced analysis into one easy-to-learn user environment for high productivity. Extend your possibilities with the Python coding feature and a multitude of supported libraries and APIs. Optional Virtual Reality interface.

placeholder40px ZEISS arivis Cloud Train Deep Learning models to automate your image analysis in ZEISS arivis Cloud (formerly APEER). Whether you use standard pipelines for routine tasks or create your own application, you can power your research with AI with just a few clicks. You can train your own model or alternatively, select a pre-defined pipeline and use a previously trained model on your images. The AI-trained models can be used with other ZEISS software products. Read More

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