CryoET Data Portal

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

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.

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 can be filtered by specifying a regular expression pattern.

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

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

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

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.

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.