quoll

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

2. Pip install

pip install quoll

Developers

1. Clone the repository. In a terminal:

git clone https://github.com/rosalindfranklininstitute/quoll.git

2. 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

3. 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.