CryoET Data Portal

napari-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_043

Installation

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.

Usage

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

https://github.com/chanzuckerberg/napari-cryoet-data-portal/assets/2608297/51207e08-68af-446a-87bb-3de9c6756d35

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

Connect button and URL to the portal

You can optionally query a subset of datasets, runs, voxel spacings, or tomograms using their corresponding IDs. This can speed up the listing process as the portal grows. To do so, select an ID type in the associated drop-down box from this panel, then enter the IDs of interest separated by commas in the text box next to it. For example, if you only want to list datasets 10000 and 10001, select Dataset IDs from the drop-down box and enter the text 10000,10001 in the text box. By default, all datasets are listed.

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. By default, opening a new tomogram clears all the existing layers in napari. If instead you want to keep those layers, uncheck the associated check-box in this panel.

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

Contributing

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 opensource@chanzuckerberg.com.

Security

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

License

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.

Acknowledgements

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

Version:

  • 0.3.0

Last updated:

  • 31 January 2024

First released:

  • 14 August 2023

License:

Supported data:

  • Information not submitted

Open extension:

GitHub activity:

  • Stars: 5
  • Forks: 1
  • Issues + PRs: 7

Python versions supported:

Operating system:

Requirements:

  • cryoet-data-portal ~=3.0
  • fsspec[http,s3]
  • npe2
  • numpy
  • napari-ome-zarr
  • ndjson
  • qtpy
  • superqt

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