GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

TL;DR

GENFIRE is a novel iterative Fourier-based algorithm that enhances 3D tomographic reconstructions from limited projections, improving accuracy and reducing human intervention across scientific fields.

Contribution

The paper introduces GENFIRE, a new Fourier iterative reconstruction method that improves 3D imaging quality from limited data with minimal user input.

Findings

GENFIRE outperforms existing reconstruction techniques in simulations.

It successfully reconstructs 3D structures of porous materials and cyanobacteria.

The algorithm incorporates angular refinement to reduce tilt errors.

Abstract

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.