Home / MIAP ZEISS OAD & APEER Workshop


The goal of this 4-day workshop is to teach and train participants how to employ the ZEISS software ecosystem for their own projects in image processing, analysis and microscope automation.

We will discuss the latest developments in image analysis and machine learning, including the novel free image processing platform APEER, which enables users to exchange image processing modules and assemble them into powerful processing workflows. You will learn how to use APEER in the cloud and how to set up a local APEER solution based on the ACQUIFER HIVE system.

We will show best practices and application examples in a hands-on session focused on:

  • How to automate image acquisition and analysis using OAD scripts (Open Application Development)
  • How to set up adaptive feedback experiment workflows in combination with APEER, Fiji/ImageJ etc.
  • How to leverage the full potential of ZEN Blue and 3rd party image processing in your image processing and analysis workflows
  • How to create your own APEER modules
  • How to build your own local APEER server using the HIVE solution from ACQUIFER.


The workshop will include lectures, discussions and extensive hands-on sessions using the microscope infrastructure of the Life Imaging Center (LIC).
Participants are invited to give a talk about their workshop-related projects, research (requirements) and custom solutions.
Participants are also encouraged to bring their own samples or experimental workflows, discuss them with the teachers and derive custom solutions for their individual microscopy and image analysis challenges. Please contact us in advance about the prerequisites.

Basic knowledge in light microscopy and scripting is required.


More information:

The ZEN Blue software is a powerful and flexible microscopy software for image acquisition and analysis. Its Open Application Development (OAD) interface allows for automation of workflows to create advanced experiments that link image acquisition and analysis. This allows for example to track migrating or growing cells or change imaging parameters depending e.g. on cell morphology changes during image acquisition.

Open Application Development (OAD) uses powerful Python scripts inside ZEN Blue to simplify, customize and automate your workflows. The CZI-API and BioFormats allow to access CZI files from external applications. Users can analyze and exchange their data with other external applications (e.g. FiJi, Python, CellProfiler, Matlab, Excel,…). OAD allows to create “smart” experiments with Exp. Feedback and Exp. Designer and to modify the acquisition on-the-fly based on online image analysis and external inputs.


The registration fee of 100 € per person covers lunch (finger food), refreshments and coffee & tea breaks with some snacks and sweets for all days of the workshop.


Albert-Ludwigs University Freiburg
Life Imaging Center (LIC)
Center for Biological Systems Analysis (ZBSA)
Habsburgerstr. 49
79104 Freiburg im Breisgau


Microscopy and Image Analysis Platform (MIAP)

Tobias Wernet
e-mail: tobias.wernet@zbsa.uni-freiburg.de

Sibylle Bartsch
e-mail: sibylle.bartsch@zbsa.uni-freiburg.de

Carl Zeiss Microscopy GmbH

Marion Lang
e-mail: sebastian.rhode@zeiss.com

Sebastian Rhode
e-mail: marion.lang@zeiss.com


Workshop Details

November 4th – 7th 2019