Artis Tomo

Computational methods for tomography and microscopy.

Description

Artis Tomo is a collection of algorithms, methodologies and programs to process and analyse imaging and tomographic data from X-ray and electron microscopies, among others.

Source code

Artis Tomo is open source and is available at GitHub.

Installation

It is available at PyPi and can be installed with pip as:

$ pip install artis-tomo

GPU acceleration

Artis Tomo is also compatible with GPU acceleration. In case you use a machine with an Nvidia GPU and CUDA capability, you can make it available by creating a conda environment:

conda create -n artis-tomo
conda activate artis-tomo
conda install -c conda-forge cudatoolkit cupy
conda install rapidsai::cubinlinker conda-forge::ptxcompiler
pip install artis-tomo

Or a micromamba environment:

micromamba create -n artis-tomo python=3.9
micromamba activate artis-tomo
micromamba install -c conda-forge cudatoolkit cupy
pip install ptxcompiler-cu11 cubinlinker-cu11 --extra-index-url=https://pypi.nvidia.com
pip install artis-tomo

When installing cupy or cudatoolkit, try the most suitable versions for your hardware.

Programs

ars_corr_fluo_2d
ars_corr_fluo_3d
ars_tomo_import_imod

Usage

ars_corr_fluo_3d -i imod_folder -m xray_mosaic.tiff -f 3DSIM_BR_FL_SIR.dv --xrpix 10
--mpix 20 --flpix 60 --flzpix 120 --channel 1 --range 600 1200 -o corr3d/ --gpu 0 --nproc 8 --tomofn xray_nice_sirt_rec.mrc

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.