Data Management for the Core Imaging Facility

Scale your data workflow

The scale of image generation in the core lab has increased exponentially. This increase has been fueled not only by developments in instrumentation capability but also by improvements in approaches to sample management, staining, long term or correlative acquisitions, and smart imaging routines. The step change in terms of data volumes places data management at the heart of the core lab. The data management workflow, from acquisition of images to subsequent storage, visualization, processing, and analysis, is a key consideration, and providing powerful and scalable solutions is vital.

Data Storage

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 to the imaging data in the short-to-long-term 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.

Store and access your data from anywhere in the facility and share your TB datasets with your collaborators anywhere at anytime using a simple weblink

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 of your facility instruments and offline workstations so your users save their data in one place and access it from any machine without the need of making copies. You can control the access rights and size of the storage available for each of your users with a few mouse clicks

ZEN Data Explorer is the web browser interface that allows data to be remotely accessed from anywhere at anytime. Consult and discuss your terabyte datasets with collaborators around the globe in real time!

This simple Windows-based server solution provides an easy and scalable way to manage your users’ data, preventing multiple copies of the same dataset, and ensuring traceability.


As imaging instrumentation develops, so 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 the challenging datasets of tomorrow goes a long way towards ensuring users can “see” what they need to from their samples to complement the quality acquisitions from your facility instruments.
ZEISS has partnered with arivis to deliver a range of tools built to manage your large datasets. Read on to learn more about the best solutions for image analysis for your core lab.

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


ZEN software comes complete with the built-in 3D visualization engine designed by arivis. This ensures smooth 3D handling of datasets up to ~100 GB in the familiar interface of ZEN.  

ZEN lite

In addition to ZEN, 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.

ZEN Logo

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 of processing and analysis are all key in ensuring the most optimal experimental outcomes for your facility’s users. However, the variety of processing and analysis approaches is vast and rapidly developing; keeping pace with the best approaches can be a challenge.

Using “black box” processing or analyses where approaches are unknown or unpublished generates significant uncertainty about results and can lead to challenges during publication. The ideal solution is to use methods that are publicly available so that there is complete transparency of image processing and reproducibility can be guaranteed.

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

ZEISS offers a selection of image analysis choices that are either contained within the acquisition software, provided by 3rd party partners, or custom designed within APEER, the ZEISS processing and analysis platform. Combining the familiarity of the acquisition platforms for a significant number of processing tasks with the flexibility and capability of solutions from our partners, as well as the future proofed APEER ecosystem, ensures you can advise your facility users regarding the solution that is most appropriate for their requirements. This flexibility comes with the assurance that any new analysis function that is programmed in the APEER community or by collaborators today can be quickly and easily integrated into your user’s workflows tomorrow without the requirement of any programming knowledge at all.

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

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 pace with the numerous developments and approaches to machine learning is key in providing the optimal results for users of your facility. 

ZEISS provides a flexible variety of machine learning tools to suit all applications. 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 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.  

Machine learning is a powerful and increasingly common means of segmenting images prior to analysis
Machine learning is a powerful and increasingly common means of segmenting images prior to analysis. 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.