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 ZEN SOFTWARE TOOLKITS

Developer Toolkit for Life Science Research

Software Integration and Customization

Modern imaging experiments often need connected accessory devices. Your workflow may also require advanced functionality available in FIJI and Python, but not in ZEN. Pushing the boundaries of experimental automation, ZEN Developer toolkit now enables smooth integration of external tools in ZEN, or vice versa.

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  • Numerous diverse interfaces
  • Scripting interface with integrated IDE
  • Instrument control from external software
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Numerous Diverse Interfaces

The Many Ways of Interacting with Your Instrument

There is a number of different ways of accessing ZEN, including instrument control, from external tools. Open Application Development (OAD) allows workflow customization, automation and execution of external analysis (e.g. in FIJI or Python). COM and TCP/IP interfaces allow remote instrument control from external applications. Advanced applications can be developed with ZEN extensions.

Scripting Interface with Integrated IDE​
Scripting Interface with Integrated IDE​

Scripting Interface with Integrated IDE

Full Workflow Customization via ZEN‘s Own Scripting Tool

At the heart of the Developer Toolkit is the ZEN’s integrated development environment (IDE) for IronPython scripting. It allows importing of IronPython packages and .NET libraries. The light-weight IDE enables recording of manual workflows in ZEN, code editing with Intellisense code completion and debugging. Almost any ZEN hardware control or analysis function can be employed, and external analysis software may be executed from within the scripts.

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Instrument Control Through External Software

Full Workflow Customization via ZEN’s Remote Control

If you want to integrate imaging into your custom workflows, you may easily control ZEN remotely using external software. ZEN has implemented the user-friendly TCP-IP and COM interfaces, enabling receiving receipt of external ZEN PythonScript commands. This means you can now easily send individual commands or even entire OAD macros with minimal overhead effort.

ZEN Macro IDE - Features and Boilerplates

    • Code Completion

      Code Completion

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      Macro editor's code completion accelerates script coding by suggesting object variables and methods, minimizing typos.
      Code Completion

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      Macros automate and customize imaging workflows, granting access to and control over hardware parameters on imaging systems.
      Hardware Control

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      Automate and customize image processing workflows with macros. Access almost all functions, including image analysis, BioApps, Intellesis, and more in ZEN.
      Processing and Image Analysis

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      Create interactive user input scripts with ZEN's API. Define and access experimental parameters through text fields, drop-down menus, and UI elements.
      Simple GUI creation
    • IronPython Functionality

      IronPython Functionality
    • Run External Applications

      Run External Applications
    • Importing Plots to ZEN

      Importing Plots to ZEN
    • Integrate Macros

      Integrate Macros

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      ZEN's macro editor, built on IronPython for .NET scripting, is compatible with CPython 2.7 and .NET assemblies, allowing for complex macro creation.
      IronPython Functionality

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      Integrate image processing from an external software with ZEN's macro editor with just a few lines of code.
      Run external applications

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      Round up customization workflows by re-importing external plots or graphs . ZEN reads typical data formats such as PNG or JPEG.
      Importing Plots to ZEN

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      Hardwire your new macro into the ZEN UI and use it regularly. It appears as a clickable button in the panel above the image viewer.
      Integrate Macros

Scripting Resources

Tutorials, Templates, Programming Environments, and User Forums

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OAD Github Page – Scripts for ZEN applications

Tutorials, Templates, Programming Environments, and User Forums

OAD's GitHub page provides scripts to automate ZEN applications like BioApps, Experiment Feedback, Guided Acquisition, Intellesis Machine Learning, ZEN Connect…

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OAD Github page – Templates for SW interfaces

The GitHub page has scripts for third-party integration (FIJI, Python, Napari, Matlab, Jupyter notebooks) covering image import/export, COM/TCP-IP interfaces, and CZI image format reading.

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OAD Github Page – Google Colab Workspace

GitHub's Jupyter Notebook scripts are accessible in Google Colabs, allowing interactive learning through well-documented scripts. These run on Google's cloud with GPU support, ideal for machine learning.

ZEISS Microscopy Developer Community ​

ZEISS Microscopy Developer Community

For OAD scripting discussions and assistance, ZEISS Microscopy hosts a forum where users engage, post questions, and receive prompt feedback from both peers and ZEISS experts.

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