ZEN Microscopy Software

This new processing algorithm for Apotome datasets enables confocal-like image quality on widefield microscopes:

• Lateral resolution down to 180 nm 
• Increased axial resolution
• Increased signal-to-noise ratio (SNR)
• Fully integrated in ZEN Direct Processing & Batch Processing workflows
  

This new ZEN acquisition module enables NLO-FLIM (nonlinear optical fluorescence lifetime imaging microscopy) on ZEISS LSM 980 systems.

• Compatible with single- or dual-line excitation
• Single- or dual-channel non-descanned detection
  

This module extends the possibilities of ZEN lite – the free version of ZEN for basic image acquisition and analysis – to control microscopes with coded components:

• Readout, display, and adjustment of encoded microscope configurations in ZEN lite
• LED light source control with ZEN lite
  

ZEISS Viluma is a family of light sources for fluorescence imaging that provides you with all the benefits of advanced LED technology. With the integration of the new light sources in ZEN 3.11, you can unlock their full potential across the entire ZEN ecosystem and the ZEISS portfolio of widefield microscopes.

The ZEN 3.11 release continues the performance enhancement of Instance Segmentation:

• Faster time to result in all workflows that include Instance Segmentation
• Faster training speeds
• Faster model download between ZEISS arivis Cloud and ZEN
  

After optimizing the Deep Learning training performance in the previous version, this release now adds accelerated model employment. You will benefit from:

• Better time-to-result for Instance Segmentation​
• Faster inference also in Image Analysis Wizard, Bio Apps, and Guided Acquisition workflows
  

As a user of the Bio Apps Toolkit, you can now analyze nuclear translocation of molecules. The new method comes with:

• Simple, one-step setups​
• A dedicated result view including multi-well plate heatmaps​
• The option to integrate advanced Deep Learning segmentation
  

Lattice SIM processing has been implemented as a feature of Direct Processing. When performing SIM² processing workflows, you will benefit from:

• Improved time-to-result​
• Increased computational resources by parallel processing on a dedicated processing workstation​
• Intelligent data compression for faster file transfers
  

On widefield modalities, users of the AI Toolkit can now employ Noise2Void Deep Learning during Continuous Acquisition Mode. This enables:

• Efficient live denoising with best-in-class algorithm​
• Sample exploration with quality images under mild illumination settings​
• Reduction of phototoxicity and bleaching
  

Instance Segmentation has received important updates that will boost your segmentation quality and time-to-result:​

• ​Significant reduction of model training times​
• Multi-channel Instance Segmentation models in ZEN Image Analysis​
  
• Random object coloring for visualizing dense objects
• Remote model download for systems with restricted internet access
  

Fast, lossless compression with Zstd is now available as standard for image acquisition with ZEN. ​

• ​With compression rates between 2X and 20X, you will benefit from fast file transfer rates and reduced data storage costs.
• For effortless batch compression of existing data archives, use our free standalone tool CZI Shrink
  

With this release, Direct Processing has received the following improvements:

• Reduce the computational load on your acquisition system by running AI Denoising and Linear Unmixing (for LSM Spectral Imaging) on a remote workstation.
• Direct Processing is now compatible with mixed mode acquisition on LSM systems and Celldiscoverer 7.​
  

Your correlative imaging will benefit from the latest additions to the ZEN Connect toolkit:​

• ​Dynamics Profiler is now integrated into the Connect workspace.​
  
• Publication-ready screenshots can be created from multi-volume 3D data.​
  

Simplify your ZEN start-up​
Start-up of ZEN with the appropriate profile has been further simplified. While ZEN configured itself based on available (partially complex) licenses in the past, it now directly accesses available MTB ZEN profiles to choose from.​

Bigger data. Faster processing.​
With ever-increasing data sets, large data handling remains a key topic for microscope users. The ZSTD lossless compression can now be set as default for image acquisitions, leading to higher file transfer rates and optimized data storage. Furthermore, algorithms for maximum intensity projections, tiles stitching, and image pyramids generation have been significantly accelerated.​

Faster and more automatable image pre-processing​
The largely popular workflow tool Direct Processing has received another addition to its toolset. With ZEN 3.8 you will be able to include stitching directly into your automated acquisition workflows, while simultaneously benefit from performance gains by algorithm optimization and parallel processing.​

The segmentation revolution continues…​
Instance Segmentation is now available for annotation and training on the arivis AI cloud platform. Within ZEN, the Image Analysis Wizard and the Bio Apps Toolkit are ready for integrating this new AI functionality into your workflows. Instance Segmentation solves the problem of precisely separating objects even in close vicinity to each other, without relying on error-prone and limited watershed algorithms.​

Gain user flexibility and better use of workstation resources
The introduction of Floating Licenses for ZEN and its toolkit packages expands the usage models in your institution. Where ZEN users were formerly restricted to a particular workstation, you are no longer limited and may now use your infrastructure resources much more flexibly.

Use the full potential of your imaging system
Advanced imaging systems acquisition rates can easily outpace data storage speeds, thereby limiting large data experiments. ZEN is now equipped with lossless and fast Zstandard compression. Up to 20-fold compression ratios accelerate data storage and optimize data economy. Zstandard comes built-in with both the Direct Processing module and ZEISS Lattice Lightsheet 7 systems. It is also optionally available for any data in .czi format.

Improvements for Guided Acquisition workflows
The Guided Acquisition module has been equipped with new features to perform even more complex Smart Imaging workflows. For this, it now comes with fully developed class selection in the Image Analysis Wizard and allows precise adjustments on how much detailed acquisitions should be run.

Open Model architecture enables model exchange
Deep Learning tools have become ubiquitously available in image analysis software, and the ZEISS software portfolio is no exception. To foster simple model exchange, ZEN and Vision4D are compatible with APEER Deep Learning and 3rd party models. Apply your favorite models in established workflows free of charge.