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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


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