Skip to main content

Image quality assessment for electron tomography

Project description

quoll

DOI napari hub

Image quality assessment for electron tomography

Installation

Users who prefer graphical user interfaces (i.e. Napari)

Find Quoll's Napari plugin (napari-quoll) here

Users (pip)

  1. Create a new conda environment, name it whatever you'd like, but don't forget to activate it
conda create -n quoll python=3.7
conda activate quoll
  1. Pip install
pip install quoll

Developers

  1. Clone the repository. In a terminal:
git clone https://github.com/rosalindfranklininstitute/quoll.git
  1. Navigate to the Quoll directory and create a new conda environment for Quoll. Don't forget to activate this environment
conda env create -n quoll python=3.7
conda activate quoll
  1. Pip install the quoll package
pip install -e .

Examples

The examples folder contains Jupyter notebooks for example usage.

Alternatively the tests also go through some ways of using quoll.

CLI Usage examples

To use the one-image FRC in the command line, once Quoll is installed.

oneimgFRC -h

brings up the help options for the one image FRC

To run the one image FRC on a single image without tiling (i.e., estimate resolution of the entire image),

oneimgFRC <image_filename> <pixel_size>

To run the one image FRC on a single image split into square tiles of length n pixels,

oneimgFRC <image_filename> <pixel_size> --tile_size <n, e.g., 128> --tiles_dir <tiles_dir>

The resolution results, resolution heatmap, and the overlay of the resolution heatmap on the image can be saved with the flags --save_csv, --save_overlay, --save_heatmap.

The resolution heatmap overlaid on the original image can be displayed with the --show_plot flag.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

quoll-0.0.4.tar.gz (19.0 kB view details)

Uploaded Source

Built Distribution

quoll-0.0.4-py3-none-any.whl (21.2 kB view details)

Uploaded Python 3

File details

Details for the file quoll-0.0.4.tar.gz.

File metadata

  • Download URL: quoll-0.0.4.tar.gz
  • Upload date:
  • Size: 19.0 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for quoll-0.0.4.tar.gz
Algorithm Hash digest
SHA256 d45fbea5e62ddef94e60a888637333700a5422279409e7478b9c65e055e8121b
MD5 eca8044499536b3489a98a23f7acb99b
BLAKE2b-256 8eeea710442d26a0607fb78c08cb50f00c5a8140a31975761377067048cbab8b

See more details on using hashes here.

File details

Details for the file quoll-0.0.4-py3-none-any.whl.

File metadata

  • Download URL: quoll-0.0.4-py3-none-any.whl
  • Upload date:
  • Size: 21.2 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for quoll-0.0.4-py3-none-any.whl
Algorithm Hash digest
SHA256 497633e70fff9bbc8830143777f93b630ed875d7f5ef5d156dceb6727ada1f72
MD5 6fd564bd2f63f7fdd3f5707d6e475f50
BLAKE2b-256 ab4d2d0ca23267ca59bdad86357fd54586c089a66e79d0a57d3e6c80471dc32e

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page