APEER Machine Learning

We are thrilled to announce the addition of machine learning tools to APEER. APEER ML makes deep learning based semantic (pixel) and instance (object) segmentation easy.

Learn more


Create your own imaging modules using the programming language of your choice, as we use Docker, or build on others’ work.


Combine private and public image processing modules into customized solutions. Automate the workflows for increased productivity and reproducibility.


Save valuable research time by not reinventing code. Share work with your team or with the community. Work from anywhere using any device.

APEER Image Processing Machine Learning Modules
APEER Image Processing Community
PEER Image Processing Workflow Machine Learning Viewing Results
APEER Customized Image Processing Solution

Seamlessly combine discrete imaging modules into a meaningful workflow.

Your customized image processing solution






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Create and customize image processing workflows.
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Automate your workflows to increase productivity.
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Make your experiments reproducible, by you and others.
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Share your work with individuals or the entire community.
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Collaborate with other researchers to complement your skillset.
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Gain visibility by sharing your work with the imaging community.
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Implement code independently of the programming language as we use Docker.
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Use our free GPU resources for your machine learning modules.
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Do not reinvent code. Build on others’ work.
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Share your work with the entire community or with select individuals in your team.
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Solve real-world problems by collaborating with researchers.
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Preserve the knowledge of your team by archiving their workflows and results.
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Foster collaborations across your institute.
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Provide visibility to your institute’s solutions after publication.
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Free up your microscopes by running analysis in the cloud.
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Easily scale up your analysis resources.
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Save training time by providing readily usable workflows to all team members.
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Receive customized solutions for your specific jobs, from imaging to reporting.
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Use intuitive interface to get quality results from both engineers and operators alike.
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Standardize your image processing pipelines to ensure consistent results between operators and sites.
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Scale computations on-demand using cloud resources.
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Not ready for cloud yet? Use our hybrid solution to keep your data and results locally.
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Need more information? Write to us at support@apeer.com





You are a researcher

Mobilize the coding power of developers around the world to address your research problem.

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You are a developer

Reveal your skills and develop solutions to real research problems.

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The platform

APEER Platform Illustration

It is a simple idea that drives us: Imaging Specialists are handling up to five different software solutions in order to create one good workflow. That workflow runs locally somewhere and is not shared. Imaging student with no prior coding knowledge are thus struggling with their image processing tasks. We want to change that! APEER is an initiative started by ZEISS to offer customizable solutions to the microscopy community.

Business model


There will always be a free version - APEER Core. Due to our users’ higher demand in storage and processing power, we are working on a subscription based Pro version, which will be rolled out soon.  

A ZEISS Initiative


APEER is fully funded and supported by ZEISS. This does not mean it is only for ZEISS customers using ZEISS microscopes. APEER has modules to read most file formats, including ZEISS’ own CZI format. That said, if you have a ZEISS microscope running ZEN 2.6 or later, you can trigger workflows directly from ZEN instead of logging on to the platform from apeer.com and uploading files manually. The integration with ZEISS microscopes will get strong in future based on your feedback.

Intellectual property 


Your intellectual property rights are fully protected while using APEER. This includes all your data (images and results), modules and workflows on the platform. For statistical purposes as well as for improving the platform services for our customers, we may occasionally use anonymized data.

Cloud and data confidentiality


Data security is a top priority for us. We utilize latest security mechanisms provided by Microsoft Azure. Your files can only be accessed by you and whoever you have chosen to share the data with. As long as your code is in a private module, only technical support staff can have access to it if need be.

Cloud and data size


The computing resources are configurable. Current setup is 12 GB of RAM and guaranteed 1 CPU and maximum of 3 CPU units based on the current system utilization. The same parameters are used for GPU units. Our GPU unit is NVIDIATesla K80. You have 100 GB of storage capacity with the free version of APEER. If you want to accelerate your computation you can create modules which run on GPU.


OME-TIFF standard

To streamline the compatibility of APEER modules we settled on using OME-TIFF as a default recommended file format. Our goal is to make it as easy as possible for you to create custom workflows – therefore we want to have all modules supporting the OME-TIFF file format so that they can work together in a reliable way.

Rolled out

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Module creation

We are working hard on optimizing the Module building experience. It's our goal to make it much easier and faster to build a Module, even without programing skills. This feature will also allow you to get existing code much faster on APEER making it possible to combine it with other Modules.

Result viewer

You are now able to view and download module results directly when running a Workflow. All file outputs and even non-file outputs can be previewed while your workflow is still running. This makes it possible to check intermediate results without waiting for the whole workflow to finish and will make it much easier and faster to optimize your workflow parameters to fit to your needs.

Rolled out

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Denoising images using kuwahara filter

How-Tos | Feb 20, 2020

Training Artificial Neural Networks

Image processing | Apr 6, 2020

Why the future of microscopy is computational

Image processing | Jun 10, 2020

APEER stories

“APEER is just the solution we need. Actually, if APEER wouldn't exist, we would probably have to develop it on our own.”

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Watch the video

Prof. Dr. Ralf B. Wehrspohn

Director Institute for Microstructure of Materials and Systems IMWS

“As microscopists, we built the platform we always wished for. A platform that lets any researcher customize and automate image processing tasks regardless of their coding skills.”

Sreenivas Bhattirpolu

APEER Academia Key Account Manager

Sreenivas Bhattirpolu APEER product owner

Our partners

These teams are using APEER to their advantage.

BMW logoJawaharlal Nehru Centre for Advanced Scientific Research logo
Vilniaus universitetas logoFraunhofer logo

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