APEER - New Annotation Tool for Machine-Learning

Hi all,

we just released our new web-based annotation tool for machine-learning as part of the APEER platform. All the information can be found here:


With the annotation tool you can…

  • … easily create your own training datasets by painting pixels
  • … annotate multidimensional datasets
  • … work online and annotate your images on the go
  • … export the images to use the annotations for your training

The tool is free for academia, non-profit, and individual use. To try it out with the demo images you do have to sign up but testing it on your own images requires signup.


I am trying it now, thanks.
Can we say that is the online version of AIIS in ZEN Intellesis ? or is there any difference between them?

  • Abdullah


the Annotation Tool is part of the APEER platform and is an really only for Annotation (at least as of today). Right now there is not direct link to ZEN Intellesis, which is the ML Segmentation Tool for Pixel Classification using RF Classifier or pretrained neural networks. (We offer pretrained UNet for Nucleus Detection or even Training your network as a paid service

But in the future those things will surely come together.

  • on APEER we work on integrating ML training pipelines that can use the labels created with Annotation tools (future)

  • additionally we will use the public python package czmodel to package trained models in a way the can be used directly in ZEN intgerated into Intellesis and all other Image Analysis Tools incl. GPU support and Tiling / Fusion Client

  • the model import is described on our Github page and an example notebook allows you to get started easily

  • the ANN model specification and the model import in ZEN can be used for any model compatible with ZEN (we currently use TF2.SavedModel as our standard format)

So a possible workflow (as of today) would be:

  • label your images on APEER
  • export the data and train your network where you like (or create/use an APEER module for it)
  • use your network wherever you like or …
  • … if you like the comfort and features (Tiling, Class Segmentation, integration with IA or Guided Acquisition etc.) in ZEN, use the czmodel package to “package” your network into a *.czmodel (just a zip file) and use in ZEN

Remark: The Import of externally trained models in ZEN required ZEN blue 3.2 (to be released within the next days) or ZEN core 3.1 (to be released by the end of summer 2020


Can I use APEER for the analysis of imaging mass cytometry data?


Thanks, sebi06, for this information.

I signed up but I received no email from APEER to verify my account. What do you think I should do?

For those who are interested learning how to use this tool, please watch our recorded tutorials.

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