Core Imaging Facility Data Management
Core Imaging Facilities

Data Management

Stay ahead of user requirements for larger and more complex datasets

The scale of image generation in the core lab has increased exponentially. Developments in instrumentation capability as well as improvements in approaches to sample management, staining, long-term or correlative acquisitions, and smart imaging routines all contribute to increasing data volumes. To support this deluge of data generation, the process of data management now sits at the heart of the core lab. The data management workflow, from acquisition to subsequent storage, visualization, processing, analysis and sharing is a key consideration. Providing solutions that are both powerful and scalable enables core imaging labs to keep pace with the ever-growing data needs of facility users.

Data Storage for Traceability and Accessibility of Large Data Sets
Data Storage for Traceability and Accessibility of Large Data Sets

Data Storage for Traceability and Accessibility of Large Data Sets

The optimal scenario for the management of data in the core facility is when images are “stored once and never moved.” This approach to data management not only ensures easy and reliable access but also supports the drive to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets (FAIR Data).

Interfacing core lab data management solutions with institutional IT infrastructure can be challenging, especially when it comes to topics such as security and the sheer volumes of data involved. It can also be challenging to invest in the IT personnel necessary to maintain complex servers and associated data management software.

ZEISS ZEN Data Storage together with a Windows server provide your answer. ZEN Data Storage is remotely installed in less than 30 minutes. The server network connects all your facility instruments and offline workstations so your users save their data in one place and can access it from any machine without the need of making copies. You control the access rights and size of the storage available for each of your users and the solution comes with a web browser interface that allows data to be remotely accessed from anywhere. Use this solution to consult and discuss your datasets with collaborators around the globe in real time.

If you plan to combine central storage with central processing or are implementing your data management workflows in the cloud, then arivis VisionHub is a powerful solution for managing your processing and analysis needs. This scalable solution to data management is the ideal tool for demanding applications such as high content screening and provides a central nucleus for data management to support facility users’ needs.

Selecting the optimal solution for managing user data in the facility is vital to prevent multiple copies of the same dataset and to ensure traceability, accessibility and scalability.

Powerful visualization of big data using arivis Vision4D; Sample courtesy of Erin Diel, Harvard Center for Biological Imaging

Visualization of Large and Complex Datasets

As imaging instrumentation develops, the resulting datasets increase in volume and in the number of dimensions. Handling these datasets for visualization in 3D, 4D, or 5D becomes an ever-increasing computational challenge. Ensuring you have software tools available in your facility to cope with data sizes and volumes is critical to enable your users to visualize and subsequently quantify the structure or events of interest in their multi-dimensional datasets. A combination of high-power computing as well as software optimized to quickly manage these datasets is critical to ensure that your users can “see” in full detail the data they acquired with your instrumentation.

Depending on the size and scope of requirements, ZEISS has different recommendations for data visualization:

  • arivis Vision4D: Your modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size. If your users regularly work with datasets of more than 100GB, arivis Vision4D is ZEISS’ recommended solution. The unique ImageCore technology is RAM independent, and this ensures that arivis Vision4D gives you and your users the power to handle datasets without constraints.
  • ZEISS ZEN Software: The user interface used for all ZEISS light microscopes comes complete with the built-in 3D visualization engine designed by arivis. This ensures smooth 3D handling of datasets up to ~100 GB in a familiar software environment. The performance of ZEN is hardware dependent, e.g., more RAM and a faster SSD drive can significantly improve the handling of big data up to 500 GB.
  • ZEISS ZEN lite: The free 3D visualization tools available in ZEN lite are also extremely capable. This provides your users with powerful image visualization from their own computers.
Process and analyze terabytes of data with easy steps using arivis Vision4D. Movie shows 3D tracking of mRNA molecules in a zebrafish embryo. Sample courtesy of Prof. A. Oates, EPFL, Switzerland

Keeping Up with Advanced Processing and Analysis

In most cases, image acquisition is just one step in a complex experimental workflow that ultimately results in quantifiable data. How experiments are planned and configured as well as the subsequent choices for processing and analysis are all key in ensuring accurate and reproducible experimental outcomes for your facility’s users.

ZEISS offers a selection of image analysis choices including a wide range of easy-to-use solutions contained within the acquisition software, such as the ZEN Bio Apps. For applications demanding more complex analysis or involving large datasets more than 100GB in size the arivis Vision4D platform is a powerful solution. When a customized analysis approach is required the APEER platform provides a cloud-based solution that delivers full flexibility in addition to full transparency. Any new analysis function that is programmed by researchers can be quickly and easily integrated into your user’s workflows using APEER, without the need for any programming knowledge and with the assurance of full transparency in terms of processing approach.

With image processing increasingly becoming the bottleneck for gaining insight from imaging data, being equipped with the latest processing and analysis trends is key to staying abreast of the ever-changing experiments that facility users create.

Increased Efficiency and Reproducibility with Machine Learning

Providing the optimal approach to machine learning means an open architecture with multiple insertion points to meet the needs of the varying abilities of users in the facility. This image was acquired using the object classification function of the ZEN Intellesis software, which is easy to configure and easy to run.

Increased Efficiency and Reproducibility with Machine Learning

As computing power increases so too does the capability and availability of approaches to train neural networks to recognize or differentiate features of interest. Choosing the best machine learning approach for segmentation, restoration, or classification is vital for the success and reproducibility of your results. Whether the goal is segmenting particular objects of interest or identifying regions of the sample for subsequent acquisition, keeping abreast of the numerous developments and approaches to machine learning ensures you can deliver optimal results for users of your facility.

ZEISS provides a variety of machine learning tools to suit all applications. ZEISS ZEN Intellesis is a quick and easy means of training and deploying segmentation. The push-button ease of the module makes it ideal for the core facility environment when ease of use is often a key factor in onboarding users to the approach. In addition, deep learning neural networks can be trained using our APEER platform or via publicly available networks such as U-Net and then deployed using ZEN Intellesis, thus providing the most flexible approach to machine learning segmentation all within the common ZEISS user interface, ZEN.

If time or manpower is limiting, ZEISS also provides a custom service to train your neural network on your behalf so you can focus on addressing your scientific questions. Contact us if you would like to learn more about this service or if you require a customized solution.

Share this article


  • Manage cores & labs easily and focus on your research

    Infinity by Idea Elan

    File size: 435 KB
  • ZEISS Training, Education & Best Practice Sharing

    Hone Your Microscope Skills and Share Your Experiences

    File size: 957 KB
  • ZEISS Predictive Service

    Delve into the secure and sophisticated architecture of ZEISS Predictive Service with this technical overview. Designed for IT professionals, it outlines the service's secure connectivity, condition monitoring, and seamless integration into your environment, ensuring top-notch security and operational efficiency for your ZEISS microscopy systems. Discover how we prioritize data privacy and system performance, utilizing Microsoft Azure Cloud and PTC ThingWorx technologies for unparalleled data security and service reliability.

    File size: 562 KB