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(**TOM**)ography.\n\n![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/algotom/algotom/algotom_ga.yml) [![Downloads](https://static.pepy.tech/personalized-badge/algotom?period=total\u0026units=international_system\u0026left_color=grey\u0026right_color=blue\u0026left_text=Pypi-downloads)](https://pepy.tech/project/algotom) ![Conda](https://img.shields.io/conda/dn/algotom/algotom?label=conda-downloads) ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/algotom/algotom) ![Conda](https://img.shields.io/conda/pn/algotom/algotom) ![GitHub issues](https://img.shields.io/github/issues-raw/algotom/algotom) ![Conda](https://img.shields.io/conda/dn/conda-forge/algotom?label=conda-forge%20downloads) ![Coverage](https://github.com/algotom/algotom/raw/doc/docs/coverage_report/coverage.svg)\n\n\n![logo](https://github.com/algotom/algotom/raw/master/figs/readme/logo2.png)\n\n**Algotom** is a Python package designed for processing tomographic data. It offers a \ncomplete processing pipeline and workflow, including reading and writing data, pre-processing, \ntomographic reconstruction, post-processing, data simulation, and calibration techniques. \nThe package provides numerous utility methods to assist users in constructing pipelines \nfor processing their own data or developing new methods.\n\nKey features of Algotom include a wide range of processing methods such as artifact removal, \ndistortion correction, speckle-based phase-contrast imaging, and data reduction, as well as \nthe capability to process non-standard tomography acquisitions such as grid or helical scans.\n\nThe software stands out for its readability, minimal dependencies, and rich documentation. \nDeveloped specifically for synchrotron-based tomographic beamlines, Algotom aims to maximize \ndata quality, enhance workflow throughput, and fully exploit beamline capabilities.\n\nFeatures\n--------\n\nAlgotom is a lightweight package with minimal dependencies. The software is built \non top of a few core Python libraries to ensure its ease-of-installation. Methods distributed in \nAlgotom have been developed and tested at synchrotron beamlines where massive\ndatasets are produced. This factor drives the methods developed to be easy-to-use, \nrobust, and practical. Algotom can be used on a normal computer to process large \ntomographic data. Some featuring methods in Algotom are as follows:\n\n- Methods in a full data processing pipeline: reading-writing data, \n  pre-processing, tomographic reconstruction, and post-processing.\n  \n  ![pipe_line](https://github.com/algotom/algotom/raw/master/figs/readme/data_processing_space.png) \n \n- Methods for processing grid scans (or tiled scans) with the offset rotation-axis \n  to multiply double the field-of-view (FOV) of a parallel-beam tomography system.\n  These techniques enable high-resolution tomographic scanning of large samples.\n  \n  ![grid_scan](https://github.com/algotom/algotom/raw/master/figs/readme/grid_scan.jpg)\n  \n- Methods for processing helical scans (with/without the offset rotation-axis).\n  \n  ![helical_scan](https://github.com/algotom/algotom/raw/master/figs/readme/helical_scan.jpg)\n\n- Methods for determining the center-of-rotation (COR) and auto-stitching images \n  in half-acquisition scans (360-degree acquisition with the offset COR).\n\n- Practical methods developed and implemented for the package: zinger removal, \n  tilted sinogram generation, sinogram distortion correction, simplified form of Paganin's filter,\n  beam hardening correction, DFI (direct Fourier inversion) reconstruction,\n  FBP (filtered back-projection) reconstruction, BPF (back-projection filtering) reconstruction, \n  and double-wedge filter for removing sample parts larger than the FOV in a sinogram.\n  \n  ![pipe_line](https://github.com/algotom/algotom/raw/master/figs/readme/double_wedge_filter.jpg)\n  \n- Utility methods for [customizing ring/stripe artifact removal methods](https://algotom.readthedocs.io/en/latest/toc/section4/section4_3.html) \n  and parallelizing computational work.\n\n- Calibration methods for helical scans and tomography alignment.\n\n- Methods for generating simulation data: phantom creation, sinogram calculation\n  based on the Fourier slice theorem, and artifact generation.\n  \n  ![simulation](https://github.com/algotom/algotom/raw/master/figs/readme/simulation.png)\n\n- Methods for phase-contrast imaging: phase unwrapping, speckle-based phase retrieval, image correlation, and image alignment.\n\n  ![speckle](https://github.com/algotom/algotom/raw/master/figs/readme/speckle_based_tomography.png)\n\n- Methods for downsampling, rescaling, and reslicing (+rotating, cropping) \n  3D reconstructed image without large memory usage.\n\n  ![reslicing](https://github.com/algotom/algotom/raw/master/figs/readme/reslicing.jpg)\n\n- Direct vertical reconstruction for single slice, multiple slices, and multiple slices at \n  different orientations.\n  \n  ![vertical_slice1](https://github.com/algotom/algotom/raw/master/figs/readme/direct_vertical_reconstruction.png)\n\n  ![vertical_slice1](https://github.com/algotom/algotom/raw/master/figs/readme/limited_angle_tomography.png)\n  \n   \n\nInstallation\n------------\n\n- https://algotom.readthedocs.io/en/latest/toc/section3.html\n- If users install Algotom to an existing environment and Numba fails to install due to the latest Numpy:\n  + Downgrade Numpy and install Algotom/Numba again.\n  + Create a new environment and install Algotom first, then other packages.\n  + Use conda instead of pip.\n- Avoid using the latest version of Python or Numpy as the Python ecosystem taking time to keep up with these twos.\n\nUsage\n-----\n- https://algotom.readthedocs.io/en/latest/toc/section4/section4_5.html\n- https://algotom.readthedocs.io/en/latest/toc/section1/section1_4.html\n- https://algotom.readthedocs.io/en/latest/toc/section4.html\n- https://github.com/algotom/algotom/tree/master/examples\n\nDevelopment principles\n----------------------\n\n- While Algotom offers a complete set of tools for tomographic data processing covering \n  pre-processing, reconstruction, post-processing, data simulation, and calibration techniques;\n  its development strongly focuses on pre-processing techniques. This distinction makes it a\n  prominent feature among other tomographic software.   \n\n- To ensure that the software can work across platforms and is easy-to-install; dependencies are minimized, and only \n  well-maintained [Python libraries](https://github.com/algotom/algotom/blob/master/requirements.txt) are used.\n\n- To achieve high-performance computing and leverage GPU utilization while ensuring ease of understanding, usage, and software \n  maintenance, Numba is used instead of Cupy or PyCuda.\n\n- Methods are structured into modules and functions rather than classes to enhance usability, debugging, and maintenance.\n\n- Algotom is highly practical as it can run on computers with or without a GPU, multicore CPUs; and accommodates both small \n  and large memory capacities.\n\nUpdate notes\n------------\n\n- https://algotom.readthedocs.io/en/latest/toc/section6.html\n\nAuthor\n------\n\n- Nghia T. Vo - *NSLS-II, Brookhaven National Lab, USA*; *Diamond Light Source, UK.*  \n \nHighlights\n----------\n\nAlgotom was used for some experiments featured on media:\n\n- Scanning [Moon rocks and Martian meteorites](https://www.diamond.ac.uk/Home/News/LatestNews/2019/17-07-2019.html) \n  using helical scans with offset rotation-axis. Featured on [Reuters](https://www.reuters.com/article/idUKKCN1UC16V?edition-redirect=uk).\n \n  ![moon_rock](https://github.com/algotom/algotom/raw/master/figs/readme/Moon_rock_Mars_meteorite.jpg)\n\n- Scanning [Herculaneum Scrolls](https://www.diamond.ac.uk/Home/News/LatestNews/2019/03-10-2019.html) \n  using grid scans with offset rotation-axis respect to the grid's FOV (pixel size of 7.9 micron; \n  total size of 11.3 TB). Featured on [BBC](https://www.bbc.co.uk/news/av/uk-england-oxfordshire-49926789).\n  The latest updates on the scroll's reading progress are [here](https://www.nature.com/articles/d41586-023-03212-1).\n\n  ![herculaneum_scroll](https://github.com/algotom/algotom/raw/master/figs/readme/Herculaneum_scroll.jpg)\n\n- Scanning ['Little Foot' fossil](https://www.diamond.ac.uk/Home/News/LatestNews/2021/02-03-21.html) \n  using two-camera detector with offset rotation-axis. Featured on [BBC](https://www.bbc.co.uk/news/science-environment-56241509).\n    \n  ![little_foot](https://github.com/algotom/algotom/raw/master/figs/readme/Little_foot.jpg)  \n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falgotom%2Falgotom","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falgotom%2Falgotom","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falgotom%2Falgotom/lists"}