miss-alignment 0.1.4

She has a chaotic good alignment for tilt-series.

miss-alignment

Installation

Installation is limited at the moment to a specific python, CUDA, and torch version. This might be fixed at some point in the future. For now, its easiest to set everything up in a conda environment.

First create an environment called miss-alignment with cuda-toolkit 12.9 and activate it:

conda create –n miss-alignment –c conda-forge python=3.11 cuda-toolkit=12.9 –y
conda activate miss-alignment

We need to fix some GPU dependencies for accelerated reconstruction:

python -m pip install torch==2.8.0 numpy
python -m pip install torch-projectors --index-url https://warpem.github.io/torch-projectors/cu129/simple/

Finally install miss-alignment with this command:

python -m pip install git+https://github.com/warpem/miss-alignment.git

Check that the CLI shows up with:

miss-alignment --help

How to run?

See the docs/ folder for some barebones instructions. This will be improved soon.