Image quality assessment for electron tomography
Find Quoll's Napari plugin (napari-quoll) here
- 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
- Pip install
pip install quoll
- Clone the repository. In a terminal:
git clone https://github.com/rosalindfranklininstitute/quoll.git
- 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
- Pip install the quoll package
pip install -e .
The examples folder contains Jupyter notebooks for example usage.
Alternatively the tests also go through some ways of using quoll.
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.