NeoLlama

NeoLlama is a new tool for evaluating geometrical aspects of lamellae in cryo-ET tomograms a posteriori.

Installation

We recommend you to run NeoLlama using Python 3.12 and a miniconda virtual environment.

You can install the package by running the following commands:

cd [src_path]
conda create -n neollama python=3.12
conda activate neollama
pip install -e .

where [src_path] is the path to where you have cloned this repo.

Testing

You can run the package tests by running the following commands in [src_path]:

cd [src_path]
pytest

Using NeoLlama

In order to use NeoLlama, you must be already in the conda virtual environment

conda activate neollama

To run NeoLlama evaluations, you need a valid config file that can be generated using the command

neollama get-config

This command generates a YAML file (config.yaml) in the current working directory.

Then to run evaluation mode, simply use the command

neollama run [/path/to/images] [-f fmt] [-np np] 

where

• path/to/images can be a single image or a folder containing images for batch analysis.
• The -f flag specifies the format (extension) of the images for analysis. For example, if the given folder has both MRC and HDF5 images and you have used the -f mrc flag, then only the MRC files will be analysed.
• The -np flag specifies the number of CPUs used in parallel analysis in batch mode. Default is 1 (serial).
  Note that the number of CPU used cannot be greater than the number of images -- NeoLlama will automatically adjust the number to whichever is smaller.

Issues

Please use the GitHub issue tracker to submit bugs or request features.

Contributions

If you would like to help contribute to python-template, please read our contribution guide and code of conduct.

License

Copyright Rosalind Franklin Institute, 2026.

Distributed under the terms of the Apache-2.0 license, python-template is free and open source software.