CryoET Data Portal


List, preview, and open data from the CZII CryoET Data Portal

MIT License Python package index Supported Python versions Test status Code coverage napari hub

List and open tomograms from the CZ Imaging Institute's CryoET Data Portal in napari.

Plugin showing tomogram TS_026


You can install the latest stable version using pip:

pip install napari-cryoet-data-portal

You will also need to install napari separately as a Python package in the same environment. One way to do that with Qt included is to run:

pip install "napari[all]"

but more generally you should follow the latest napari installation instructions.


See the following video for a demonstration of basic usage of the plugin.

Click the Connect button to establish a connection to the data portal.

Connect button and editable URI to the portal

After connecting to the portal, datasets are added below as they are found.

Datasets and tomograms in the portal shown as an interactive tree

Datasets and tomograms can be filtered by specifying a regular expression pattern.

Datasets and tomograms filtered by the text 26, so that only two are shown

Selecting a dataset displays its metadata, which can be similarly explored and filtered.

Metadata of dataset 10000 shown as an interactive tree of keys and values

Selecting a tomogram displays its metadata and also opens the lowest resolution tomogram and all of its associated point annotations in the napari viewer.

Metadata of tomogram TS_026 shown as an interactive tree of keys and values

Higher resolution tomograms can be loaded instead by selecting a different resolution and clicking the Open button.

Open button and resolution selector showing high resolution

In this case, napari only loads the data that needs to be displayed in the canvas. While this can reduce the amount of data loaded, it may also cause performance problems when initially opening and exploring the data.

In general, finding and fetching data from the portal can take a long time. All plugin operations that fetch data from the portal try to run concurrently in order to keep interaction with napari and the plugin as responsive as possible. These operations can also be cancelled by clicking the Cancel button.

Progress bar with loading status and cancel button


This is still in early development, but contributions and ideas are welcome! Don't hesitate to open an issue or open a pull request to help improve this plugin.

To setup a development environment, fork this repository, clone your fork, change into its top level directory and run:

pip install -e ".[testing]"

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to


If you believe you have found a security issue, please see our security policy on how to report it.


Distributed under the terms of the MIT license, "napari-cryoet-data-portal" is free and open source software. See the license file for more details.


This plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.


  • 0.1.0

Last updated:

  • 14 August 2023

First released:

  • 14 August 2023


  • MIT

Supported data:

  • Information not submitted

Open extension:

GitHub activity:

  • Stars: 3
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

Operating system:


  • cryoet-data-portal
  • fsspec[http,s3]
  • npe2
  • numpy
  • napari-ome-zarr
  • ndjson
  • qtpy
  • superqt

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