ParticleTomography

This repository contains data and code for the paper insert title.

The algorithm is implemented in julia and was tested using the long term support version julia-1.10.

Assuming julia is installed, the project/local julia environment can be instantiated by running

julia --project=. -E 'using Pkg; Pkg.instantiate()'

from the root directory of this repository.

The experiments can be run by running julia -t auto --project=. $EXPERIMENT_FILE from the root folder of this repository. $EXPERIMENT_FILE should be replaced by one of the following:

• vesicle.jl
• vesicle_onaxis_error.jl
• protein.jl
• thinfilm.jl

The following datasets can be found in data:

• data/vesicle contains a simulated model and projection images of a biological vesicle. The dataset is taken directly and unmodified from Pham, M., Yuan, Y., Rana, A. et al.: Accurate real space iterative reconstruction (RESIRE) algorithm for tomography. Sci Rep 13, 5624 (2023) and is licensed under CC BY 4.0
• data/thinfilm contains experimental atomic electron tomography projection images of an amorphous Ta thinfilm. This dataset is also taken from Pham, M., Yuan, Y., Rana, A. et al.: Accurate real space iterative reconstruction (RESIRE) algorithm for tomography. Sci Rep 13, 5624 (2023) and is licensed under CC BY 4.0
• data/protein contains a simulated model, projection images and atom coordinates of a protein structure. The atom coordinates are taken from the protein database with entry 6B3R which is based on Yusong R Guo Roderick MacKinnon: Structure-based membrane dome mechanism for Piezo mechanosensitivity eLife 6:e33660. (2017)