How to Use APEER in Connection With ZEISS ZEN core


What is ZEN core?

ZEN core is an imaging software for connected microscopy in material labs. It supports the user by steering his microscopes as well as collecting, processing and analyzing images. The workflow based software helps the user to build his own analyzing methods step by step by choosing and putting together suitable modules from the existing supply. This generated workflow can then be used recurring for a large number of images.  

What if a workflow is needed which is not available in ZEN core

That is where APEER comes into play. The image processing platform enables users to build customized workflows for their specific tasks by creating completely new modules or using already existing modules from other users. It is also possible to combine own and public modules in one workflow. This enables customers to tailormade their application to gain efficiency and speed. For creating a new module almost any programming language code from Java to Python can be used. Scientists without coding skills can ask the APEER team or the APEER community for help to solve their research problem. For this have a look at:

How does the connection with APEER works?

To be able to use ZEN core in combination with APEER the user first has to register online on (for free). Then he can use the platform to create new workflows or build on already existing workflows from other users. The next time the user opens the ZEN core software he is able log in to his APEER account directly in the “general options” of ZEN. (For a detailed description about the usage of APEER in ZEN core, have a look at the steps below.) Now the user has access to all his private workflows which he saved in “My Workspace” in APEER and can choose any image in ZEN and upload it directly into APEER to start a new analyzing workflow. In addition, the APEER functionalities can also be linked with other ZEN core functions in a sequence like the image acquisition. In all cases the data is processed by default in the cloud. After processing, the results can be transferred back to ZEN core, e.g. to do a feedback experiment.

If the data cannot be uploaded to the cloud due to size or sensitivity reasons, there is also the option of using a hybrid solution. In this case, the data remains on the local computer and is executed there by using the online workflow. If you want to use this opportunity, please contact



1.       Log-in or register online on

2.       Build a workflow by using your own or public modules.  

3.       Save the workflow in „My Workspace“ on APEER to access it out of the ZEN core software.

4.       Log-in to APEER by using the tab in the ZEN core software (see the steps below).  

5.       Upload your microscope images in APEER directly out of ZEN core, analyze your image with the desired workflow and send the results back to ZEN core if needed.

How to log into APEER in ZEN core (detailed description):

Open the ZEN core software and go to the “Maintenance” then choose “General Options”.

ZEN Core software maintenance
ZEN Core software General Options

Now this window with all the setting options opens: here you choose the last tab called “APEER”. Then click on “connect”.

ZEN Core software settings

Now you have to put in your credentials to log-in to your APEER account.

Apeer log in tab in ZEN

After successful login your name appears in the connection state field.  

succesfull connection with APEER in ZEN Core

Now you are ready to start your image processing workflow!

If you have any further questions regarding this topic, please conntact

Roman Zinner

Content Manager

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