ZEISS Microscopy Knowledge Base
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ZEISS Microscopy Knowledge Base

Where can I use my model?

Discover how to leverage your models trained on ZEISS arivis Cloud in the ZEISS software ecosystem to get the most out of your data.

Here you'll learn about:

The ZEISS software ecosystem offers a wide variety of capabilities that can benefit from using deep learning models where conventional methods reach their boundaries. Therefore, it is a high priority for ZEISS to ensure that models trained on ZEISS arivis Cloud are integrated seamlessly within the ZEISS software ecosystem.

Simple measurements based on the segmentation results can be achieved directly on ZEISS arivis Cloud. However, the integration with complementary software, such as ZEN, ZEN core, and ZEISS arivis Pro opens the possibility to take advantage of the advanced visualization and analysis features that are available in those software solutions. Thereby, you can make deep learning models a powerful addition to your end-to-end workflow from imaging to results.

Semantic segmentation models

Semantic segmentation models trained on ZEISS arivis Cloud can be imported into ZEN, ZEN core, and arivis Pro given that the following version requirements are met.

To successfully import your semantic segmentation models make sure you have one of the following:

  • ZEN version 3.4 or newer
  • ZEN core version 3.3 or newer
  • arivis Pro 3.6 or newer

Instance segmentation models

Instance segmentation models trained on ZEISS arivis Cloud can be directly accessed from ZEN, ZEN core or ZEISS arivis Pro via the AI Model Store.

To successfully access your instance segmentation models from ZEN, ZEN core or arivis Pro make sure you have:

  • ZEN version 3.8 or newer
  • ZEN core version 3.8 or newer
  • arivis Pro 4.2 or newer

Importing semantic segmentation models

To import your semantic segmentation models trained on arivis Cloud to ZEN, ZEN core, or arivis Pro, you need to:

  1. Download your model to your computer. Here's how you can download your model.
  2. Import it into the respective software. Once the download is complete, import the file into ZEN, ZEN core, or arivis Pro.

Accessing instance segmentation models from ZEN, ZEN core or arivis Pro

The following step-by-step guide was created using ZEN as an example. ZEN core and arivis Pro provide similar functionality.

To access your instance segmentation models trained on ZEISS arivis Cloud from ZEN, you first have to link your arivis Cloud account to ZEN. To achieve that generate a unique access token (i.e., API key) on arivis Cloud and enter it into ZEN. This step only needs to be done once to access all instance segmentation models (for the time that the access token is valid). Follow the steps here to create your access token.

  1. Once you've created your access token, open ZEN and navigate to Tools > Options in the top menu.
    ZEN software interface displaying grayscale cell image with purple highlights and an Options dialog pointing to API Key field.
  2. Click on arivis Cloud (or APEER in older versions) in the menu on the left.
  3. Paste the token you've just copied into the API key field and click OK.
    Options dialog showing APEER API Key field highlighted by turquoise arrow
  4. ZEN is now authenticated to access your instance segmentation models on arivis Cloud.
  5. In the left panel, click on the Applications tab, locate the AI Model Store, and click on the arrow to expand it and see the options.
  6. Click on Download Models to access your instance segmentation models.
    ZEN interface with Download Models button highlighted by turquoise arrow and model selection dialog
  7. Select the model version you want to use in ZEN. Then simply click OK. Your model will be downloaded and listed in the AI Model Store.
    Model selection dialog showing three models with turquoise arrow pointing at First released instance seg training #1

The first time you download a model, all the code required to run the model will be downloaded together with the model. Therefore, expect longer waiting times compared to downloading additional models in the future.

Learn more

Don't forget to check out our how-to tutorial videos to see a hands-on example of how models trained with arivis AI toolkit can be used across the ecosystem.

Tutorial: How to use your models in ZEN

Have questions? We're here to help.

Have a question about using your models? Contact support team.

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