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All Projects → zeiss-microscopy → OAD

zeiss-microscopy / OAD

Licence: GPL-3.0 license
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

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Open Application Development (OAD)

ZEN Blue is an open, flexible and powerful image acquisition platform that allows controlling a wide range of microscopes systems. Additionally it offers various tools to automate microscopy workflows including acquisition, image analysis and image processing tasks.

In order to fulfill the request for automation the ZEN Blue platform offers various features and options, which are combined inside a concept called Open Application Development (OAD).

Its main components are:

  • CZI image data format and its APIs
  • Python Scripting (OAD Simple API)
  • Interfaces to ZEN (TCP-IP, COM, Extensions)
  • Experiment Feedback - Adaptive Acquistion with Online Image Analysis

OAD ToolsZEN OAD Tools

OAD - General Concept and Key Features

  • Open Application Development (OAD) uses powerful Python Scripts to simplify, customize and automate your workflows.

  • Analyze and Exchange data with applications like Fiji, Python, Knime, CellProfiler, Icy, MATLAB, Excel and …

  • API for reading CZI image data using custom software

    • ZeissImgLib (.NET) to be used on Windows-based systems
    • libCZI (C++) for cross-platform applications
    • BioFormats (CZIReader) allow easy access to CZI files from many external applications using the BioFormats library

  • BioFormats Import as a module inside ZEN Blue as well as OME-TIFF Export

  • Create “smart” experiments with Experiment Feedback and modify the acquisition On-the-fly based on Online Image Analysis and External Inputs

OAD InterfacesOAD Interfaces

Automated DynamicsAutomated Dynamics

External SoftwareExternal Software

Links and References

Disclaimer

This is an collection of tools and scripts that is free to use for everybody. Carl Zeiss Microscopy GmbH's ZEN software undertakes no warranty concerning the use of those scripts, image analysis settings and ZEN experiments. Use them on your own risk.

Additionally Carl Zeiss Microscopy GmbH's ZEN software allows connection and usage to the third party software packages. Therefore Carl Zeiss Microscopy GmbH undertakes no warranty concerning those software packages, makes no representation that they will work on your system and/or hardware and will not be liable for any damages caused by the use of this extension.

By using any of those examples you agree to this disclaimer.

Version: 2012.02.09

Copyright (c) 2022 Carl Zeiss AG, Germany. All Rights Reserved.

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