cyro-et-neuroglancer

User guide

This repository is very out of date, and only really the examples should be given any heed. The code instead now lives at https://github.com/chanzuckerberg/cryoet-data-portal-neuroglancer.

Installation

git clone https://github.com/MetaCell/cyroet-neuroglancer
cd cyroet-neuroglancer
pip install cyro-et-neuroglancer

Usage

cryoet-converter --help

Examples

See the examples folder for bash scripts that create all the necessary files for a neuroglancer viewer from a cryo-ET dataset.

Annotations

./examples/convert_and_view_image_and_annotations.sh

Segmentation

./examples/convert_and_view_image_and_segmentation.sh

Oriented points

./examples/convert_and_view_oriented_points.sh

Components

There are three parts to this package:

1. The first part of the package is designed to convert a cryo-ET dataset into a format that can be viewed in neuroglancer. The commands encode-segmentation and encode-annotation are used here.
2. The second part of the package is designed to view the converted dataset in neuroglancer. The commands create_image, create_segmentation, and create_annotation are used here. Each of these produce a JSON file that represents a neuroglancer layer. The layers can then be combined into a single neuroglancer viewer state via the combine-json command.
3. The final part of this package is designed to help quickly grab the JSON state or URL of a locally running neuroglancer instance, or setup a local viewer with a state. The commands load-state and create-url are used here.

Development

Developer installation

git clone https://github.com/MetaCell/cyroet-neuroglancer
cd cyroet-neuroglancer
pip install -e ".[dev]"
pre-commit install

Pre-commit hooks

To run all pre-commit hooks on all files run:

pre-commit run --all-files

This will lint via ruff, format via ruff (essentially black), and check mypy types with the arguments specified in .pre-commit-config.yaml.

Testing

pytest

Mypy

Manual type checking with mypy:

mypy .