Data processing (ALGO)rithms for (TOM)ography


Algotom is a Python package implementing methods for processing tomographic data acquired by non-standard scanning techniques such as grid scans, helical scans, half-acquisition scans, or their combinations. Certainly, Algotom can also be used for standard scans. The software includes methods in a full pipeline of data processing: reading-writing data, pre-processing, tomographic reconstruction, post-processing, and data simulation. Many utility methods are provided to help users quickly develop prototype-methods or build a pipeline for processing their own data.

The software is made available for [A1]. Selected answers to technical questions of anonymous reviewers about methods in the paper is here.

… Algotom development was started at the I12-JEEP beamline in 2014 as Python codes to process data acquired by the beamline’s large field-of-view (FOV) detector, which uses two imaging sensors to cover a rectangular FOV. Images from these cameras must be stitched before tomographic reconstruction can take place. Data processing methods for improving the quality of tomographic data; removing artifacts caused by imperfections of hardware components; making use the beamline capabilities; processing data acquired by non-traditional scanning techniques; and automating data processing pipeline have been actively developed at I12 over the years. These methods have been used internally by I12’s users and refined further for publication and sharing with the research community through open-source software such as Tomopy and Savu …

… In contrast to Savu and Tomopy which are optimized for speed, Algotom is a package of data processing algorithms and tools which are designed to be easy-to-use and easy-to-deploy prototype methods. The development of Algotom has focused on pre-processing methods which work in the sinogram space to reduce computational cost. Methods working in the projection space such as phase filter, distortion correction, or rotation correction have been adapted to work in the sinogram space…