A modular software framework for the design and implementation of ptychography algorithms

Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In th...

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Bibliographic Details
Published in:PeerJ. Computer science Vol. 8; p. e1036
Main Authors: Guzzi, Francesco, Kourousias, George, Billè, Fulvio, Pugliese, Roberto, Gianoncelli, Alessandra, Carrato, Sergio
Format: Journal Article
Language:English
Published: San Diego PeerJ. Ltd 25.07.2022
PeerJ, Inc
PeerJ Inc
Subjects:
Algorithms
Algorithms and Analysis of Algorithms
Computational microscopy
Computer Vision
Datasets
Decomposition
Experiments
GPU computing
Phase retrieval
Position refinement
Ptychography
Public software
Reconstruction
Reconstruction Algorithms
Scientific Computing and Simulation
Sensors
Software
Software Engineering
Software upgrading
ISSN:2376-5992, 2376-5992
Online Access:Get full text
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Summary:Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In this article, we present SciComPty, a new ptychography software framework aiming at simulating ptychography datasets and testing state-of-the-art and new reconstruction algorithms. Despite its simplicity, the software leverages GPU accelerated processing through the PyTorch CUDA interface. This is essential for designing new methods that can readily be employed. As an example, we present an improved position refinement method based on Adam and a new version of the rPIE algorithm, adapted for partial coherence setups. Results are shown on both synthetic and real datasets. The software is released as open-source.
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ISSN:2376-5992
2376-5992
DOI:10.7717/peerj-cs.1036