MUltiscale, Multimodal and Multidimensional imaging for EngineeRING

Deliverables

Demonstrators, pilots, prototypes (10)

Obtaining reproducible segmentations and assessing their statistical confidence

Methods and prototype software for obtaining reproducible segmentations and assessing their statistical confidence

Software for model-based 2D/3D segmentation with physical priors

Prototype software for model-based 2D and 3D segmentation of voxel volumes employing physical priors

Tool simulating data from physical model priors

Tool simulating both projection and reconstructed image data from physical model

Prototype software for mesh-based 2D and 3D segmentation and reconstruction

Basic Big Data platform

Training Materials for the workflow

Training Materials for the workflow framework

Fast alignment code and docs

Fast image alignment code and documentation

Training Materials for the Big Data platform

Fast Reconstruction Code and Docs

Fast reconstruction code and documentation for Task 3.1

Basic workflow framework

Other (10)

1st Summer School

1st Summer School (DTU)

3rd workshop

3rd workshop (UL)

2nd workshop

2nd workshop (FEI SAS)

4th workshop

4th workshop (AP2K)

2nd Summer School

2nd Summer School (UA)

1st workshop

1st workshop (CWI/UA)

Advertisement of vacancies

Optimized software implementation for omni-directional scattering tomography

Kick off meeting

Winter School

Winter School (AP2K)

Documents, reports (19)

Multi-scale finite element modelling procedure

Multiscale finite element modelling procedure

Protocol to acquire tilt series for multi-modal tomography

Protocol to acquire tilt series for multimodal tomography combination of electron diffraction HAADFSTEM EELS and EDX

ESR11 PhD Thesis

ESR11 DTU PhD thesis Physical model priors for tomogram segmentation

ESR2 PhD thesis

ESR2 UA PhD thesis Novel acquisition schemes for electron tomography in association with WP2 and WP3

ESR13 PhD Thesis

ESR13 UoM PhD thesis Multiscale quantification of damage in composite structures

ESR10 PhD Thesis

ESR10 AP2K PhD thesis 2D3D multimodal analysis for XRay security applications

Protocol for the acquisition of omni-directional scattering tomography

ESR6 PhD Thesis

ESR6 CWIUL PhD thesis Ultrafast Tomographic Reconstruction in association with WP1 and WP2

ESR14 PhD Thesis

ESR14 CNRS UBx PhD thesis Reactive transport in porous media A multiscale imaging and modelling approach

ESR8 PhD Thesis

ESR8 BAM PhD thesis A 3D implementation of a trained algorithm for reconstruction from limited angle projection data M39

Protocol to acquire tilt series for electron tomography using ultra-sensitive detectors

ESR12 PhD Thesis

ESR12 DTU PhD thesis Segmentation from projections

ESR1 PhD thesis

ESR1 PSI PhD thesis Time resolved omnidirectional scattering tomography

ESR9 PhD Thesis

ESR9 DTU PhD thesis 3D inversion of ptychographic tomography data in association with WP1 and WP2

Theoretical description of scattering signal dependencies

General algorithm for the coupled numerical model and super-resolution

ESR4 PhD Thesis

ESR4 UCPH PhD thesis Automated data analyses workflows for tomography data in association with WP1 and WP3

Experimental setup at the TOMCAT beamline for omni-directional scattering

Experimental setup at the TOMCAT beamline for omnidirectional scattering tomography compatible with singleshot acquisition

ESR5 PhD Thesis

ESR5 UCPH PhD thesis A Big Data Platform for storing and analyzing tomography data in association with WP1 and WP3

Websites, patent fillings, videos etc. (1)

Promotional materials (website, flyer, social media account) created

Promotional materials (website, flyer, social media account) created and actively used

Publications

Thesis dissertations (10)

Tomographic Segmentation from Limited Projection Data

Author(s): Jakeoung Koo
Published in: 2021
Publisher: Technical University of Denmark

Two examples of multi-scale numerical modelling combined with advanced X-ray based experiments: multi-scale imaging for reactive transport in porous media and X-ray beam induced current (XBIC)

Author(s): Abdellatif Saadaldin
Published in: 2022
Publisher: University of Bordeaux

Multi-modal Coherent X--ray Imaging and Tomography of Functional Materials

Author(s): Azat Slyamov
Published in: 2021
Publisher: Technical University of Denmark

Statistical Methods for Quantification and Segmentation of Material Microstructure from 3D X-ray Tomography Image Data

Author(s): Elise Otterlei Brenne
Published in: 2021
Publisher: DTU Energy

Iterative reconstruction from under-sampled Computed Tomography data

Author(s): Sotirios Magkos
Published in: 2022
Publisher: Universität Potsdam

Towards Time-resolved X-ray Scattering Tensor Tomography

Author(s): Jisoo Kim
Published in: 2022
Publisher: ETH Zurich
DOI: 10.3929/ethz-b-000548789

X-ray computer tomography based numerical modelling of fibre reinforced composites

Author(s): Auenhammer, Robert
Published in: X-ray computer tomography based numerical modelling of fibre reinforced composites, 2021, ISSN 1652-8565
Publisher: Chalmers University of Technology

MEOW - Enabling Dynamic Scheduling of Scientific Analysis

Author(s): David Marchant
Published in: 2021
Publisher: University of Copenhagen

Spectrally joint reconstruction and material classification from multi-energy CT

Author(s): Doniyor Jumanazarov
Published in: 2021, Page(s) 158
Publisher: Department of Physics, Technical University of Denmark

Grid of Clouds

Author(s): Rasmus Munk
Published in: 2021
Publisher: University of Copenhagen

Other (4)

3D atomic resolution tomography from iDPC-STEM images using multiple atommodel prior.

Author(s): S. Hosseinnejad, E.G.T. Bosch, H. Kohr, I. Lazić, V. Zharinov, E. Franken, J. Sijbers, J. De Beenhouwer
Published in: 2021 Microscopy Conference, 2021
Publisher: Universität Regensburg

Method for system-independent material classification through basis material decomposition from spectral X-ray CT’

Author(s): Doniyor Jumanazarov, Ja-Keoung Koo, Henning F. Poulsen, Ulrik L. Olsen, Mihai Iovea
Published in: 2021
Publisher: iWoRiD 2021 The 22nd International Workshop on Radiation Imaging Detectors

Significance of the spectral correction of photon counting detector response in material classification from spectral x-ray CT

Author(s): Doniyor Jumanazarov, Jakeoung Koo, Henning F. Poulsen, Ulrik L. Olsen, Mihai Iovea
Published in: Journal of Medical Imaging, 2022
Publisher: SPIE

Parallel-beam X-ray CT datasets of apples with internal defects and label balancing for machine learning

Author(s): Coban, Sophia Bethany; Andriiashen, Vladyslav; Ganguly, Poulami Somanya; van Eijnatten, Maureen; Batenburg, Kees Joost
Published in: 2020
Publisher: Leiden Institute of Advanced Computer Science
DOI: 10.48550/arxiv.2012.13346

Peer reviewed articles (29)

Material classification from sparse spectral X-ray CT using vectorial total variation based on L infinity norm

Author(s): Doniyor Jumanazarov, Jakeoung Koo, Jan Kehres, Henning F Poulsen, Ulrik L Olsen, Mihai Iovea
Published in: Materials Characterization, 2022, ISSN 1044-5803
Publisher: Elsevier BV
DOI: 10.1016/j.matchar.2022.111864

Macroscopic mapping of microscale fibers in freeform injection molded fiber-reinforced composites using X-ray scattering tensor tomography

Author(s): Jisoo Kim, Azat Slyamov, Erik Lauridsen, Mie Birkbak, Tiago Ramos, Federica Marone, Jens W. Andreasen, Marco Stampanoni, Matias Kagias
Published in: Composites Part B: Engineering, 2022, ISSN 1359-8368
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compositesb.2022.109634

MUMMERING Platform Idea’s & Ubiquitous Data Analysis

Author(s): Munk, Rasmus; Vinter, Brian
Published in: Communicating Process Architectures 2017 and 2018, WoTUG-39 and WoTUG- 40 - Proceedings of CPA 2017 (WoTUG-39) and Proceedings of CPA 2018 (WoTUG-40), 2019, Page(s) 323-333, ISSN 1383-7575
Publisher: IOS Press
DOI: 10.3233/978-1-61499-949-2-323

A physical model for microstructural characterization and segmentation of 3D tomography data

Author(s): Elise O. Brenne, Vedrana A. Dahl, Peter S. Jørgensen
Published in: Materials Characterization, 171, 2021, Page(s) 110796, ISSN 1044-5803
Publisher: Elsevier BV
DOI: 10.1016/j.matchar.2020.110796

X-ray computed tomography data structure tensor orientation mapping for finite element models – STXAE

Author(s): Auenhammer, R.M., Jeppesen, N., Mikkelsen, L.P., Dahl, V.A., Asp, L.E.
Published in: Software Impacts, 11, 2022, Page(s) 100216, ISSN 2665-9638
Publisher: Elsevier
DOI: 10.1016/j.simpa.2021.100216

System-independent material classification through X-ray attenuation decomposition from spectral X-ray CT

Author(s): Doniyor Jumanazarov, Jakeoung Koo, Matteo Busi, Henning F. Poulsen, Ulrik L. Olsen, Mihai Iovea
Published in: NDT & E International, 116, 2020, Page(s) 102336, ISSN 0963-8695
Publisher: Elsevier BV
DOI: 10.1016/j.ndteint.2020.102336

Robust numerical analysis of fibrous composites from X-ray computed tomography image data enabling low resolutions

Author(s): Auenhammer, R.M., Jeppesen, N., Mikkelsen, L.P., Dahl, V.A., Blinzler, B.J., Asp, L.E.
Published in: Composites Science and Technology, 224, 2022, Page(s) 109458, ISSN 0266-3538
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compscitech.2022.109458

Observing the evolution of fatigue damage and associated strain fields in a correlative, multiscale 3D time-lapse study of quasi-unidirectional glass fibre composites

Author(s): Anuj Prajapati, Ali Chirazi, Lars P. Mikkelsen, Timothy Burnett, Philip J. Withers
Published in: IOP Conference Series: Materials Science and Engineering, 942, 2020, Page(s) 012039, ISSN 1757-899X
Publisher: IOP Conference Series: Materials Science and Engineering
DOI: 10.1088/1757-899x/942/1/012039

Shape from projections via differentiable forward projector for computed tomography

Author(s): Koo Jakeoung, Dahl Anders, Bærentzen J.Andreas, Chen Qiongyang, Bals Sara, Dahl Vedrana
Published in: Ultramicroscopy, 224, 2021, Page(s) 113239, ISSN 0304-3991
Publisher: Elsevier BV
DOI: 10.1016/j.ultramic.2021.113239

Improving reproducibility in synchrotron tomography using implementation-adapted filters

Author(s): Poulami Somanya Ganguly, Daniël M. Pelt, Doga Gürsoy, Francesco de Carlo, K. Joost Batenburg
Published in: Journal of Synchrotron Radiation, 28/5, 2021, Page(s) 1583-1597, ISSN 1600-5775
Publisher: Wiley
DOI: 10.1107/s1600577521007153

DALM, Deformable Attenuation-Labeled Mesh for Tomographic Reconstruction and Segmentation

Author(s): Jakeoung Koo; Anders Bjorholm Dahl; Vedrana Anderson Dahl
Published in: IEEE Transactions on Computational Imaging, 25730436, 2021, Page(s) 151-163, ISSN 2573-0436
Publisher: IEEE
DOI: 10.1109/tci.2021.3052034

Multi-modal characterization of kesterite thin-film solar cells: experimental results and numerical interpretation

Author(s): Abdellatif Saadaldin; Azat M. Slyamov; Michael E. Stuckelberger; Peter S. Jørgensen; Christian Rein; Mariana Mar Lucas; Tiago Ramos; Angel Rodriguez-Fernandez; Dominique Bernard; Jens W. Andreasen
Published in: Faraday Discussions, 2022, ISSN 1364-5498
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2fd00044j

Complementary time-lapse datasets of x-ray computed tomography and real-time strain mapping for an ex-situ study of non-crimp glass fibre composites under fatigue loading

Author(s): Anuj Prajapati, Stuart Morse, Ali Chirazi, Timothy Burnett, Philip J. Withers
Published in: Data in Brief, 37, 2021, Page(s) 107157, ISSN 2352-3409
Publisher: Elsevier BV
DOI: 10.1016/j.dib.2021.107157

Dataset of non-crimp fabric reinforced composites for an X-ray computer tomography aided engineering process

Author(s): Robert M. Auenhammer, Lars P. Mikkelsen, Leif E. Asp, Brina J. Blinzler
Published in: Data in Brief, 33, 2020, Page(s) 106518, ISSN 2352-3409
Publisher: Elsevier BV
DOI: 10.1016/j.dib.2020.106518

Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabric reinforced composites

Author(s): Robert M. Auenhammer, Lars P. Mikkelsen, Leif E. Asp, Brina J. Blinzler
Published in: Composite Structures, 256, 2021, Page(s) 113136, ISSN 0263-8223
Publisher: Elsevier BV
DOI: 10.1016/j.compstruct.2020.113136

Fast acquisition protocol for X-ray scattering tensor tomography

Author(s): Kim, J., Kagias, M., Marone, F., Stampanoni, M.
Published in: Scientific Reports, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-02467-w

Three-Dimensional Quantification of the Facet Evolution of Pt Nanoparticles in a Variable Gaseous Environment

Author(s): Thomas Altantzis, Ivan Lobato, Annick De Backer, Armand Béché, Yang Zhang, Shibabrata Basak, Mauro Porcu, Qiang Xu, Ana Sánchez-Iglesias, Luis M. Liz-Marzán, Gustaaf Van Tendeloo, Sandra Van Aert, Sara Bals
Published in: Nano Letters, 19/1, 2018, Page(s) 477-481, ISSN 1530-6984
Publisher: American Chemical Society
DOI: 10.1021/acs.nanolett.8b04303

3D characterization of heat-induced morphological changes of Au nanostars by fast in situ electron tomography

Author(s): Hans Vanrompay, Eva Bladt, Wiebke Albrecht, Armand Béché, Marina Zakhozheva, Ana Sánchez-Iglesias, Luis M. Liz-Marzán, Sara Bals
Published in: Nanoscale, 10/48, 2018, Page(s) 22792-22801, ISSN 2040-3364
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8nr08376b

X-ray scattering tensor tomography with circular gratings

Author(s): Jisoo Kim, Matias Kagias, Federica Marone, Marco Stampanoni
Published in: Applied Physics Letters, 116/13, 2020, Page(s) 134102, ISSN 0003-6951
Publisher: American Institute of Physics
DOI: 10.1063/1.5145361

Quantitative Comparison of Deep Learning-Based Image Reconstruction Methods for Low-Dose and Sparse-Angle CT Applications

Author(s): Johannes Leuschner, Maximilian Schmidt, Poulami Somanya Ganguly, Vladyslav Andriiashen, Sophia Bethany Coban, Alexander Denker, Dominik Bauer, Amir Hadjifaradji, Kees Joost Batenburg, Peter Maass, Maureen van Eijnatten
Published in: Journal of Imaging, 7/3, 2021, Page(s) 44, ISSN 2313-433X
Publisher: MDPI
DOI: 10.3390/jimaging7030044

Direct Iterative Reconstruction of Computed Tomography Trajectories Reconstruction from limited number of projections with DIRECTT

Author(s): Sotirios Magkos, Andreas Kupsch, Giovanni Bruno
Published in: Review of Scientific Instruments, 91/10, 2020, Page(s) 103107, ISSN 0034-6748
Publisher: American Institute of Physics
DOI: 10.1063/5.0013111

Tomosipo: fast, flexible, and convenient 3D tomography for complex scanning geometries in Python.

Author(s): Allard A. Hendriksen; Dirk Schut; Willem Jan Palenstijn; Nicola Viganò; Jisoo Kim; Daniël M. Pelt; Tristan van Leeuwen; K. Joost Batenburg
Published in: Optics Express, 2021, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.439909

Dataset of non-crimp fabric reinforced composites for an X-ray computer tomography aided engineering process.

Author(s): Robert M. Auenhammer; Robert M. Auenhammer; Lars Pilgaard Mikkelsen; Leif Asp; Brina J. Blinzler
Published in: Data in Brief, Vol 33, Iss , Pp 106518- (2020), 3, 2020, ISSN 2352-3409
Publisher: Elsevier BV
DOI: 10.1016/j.dib.2020.106518

Suppression of Cone-Beam Artefacts with Direct Iterative Reconstruction Computed Tomography Trajectories (DIRECTT)

Author(s): Sotirios Magkos, Andreas Kupsch, Giovanni Bruno
Published in: Journal of Imaging, 7/8, 2021, Page(s) 147, ISSN 2313-433X
Publisher: MDPI
DOI: 10.3390/jimaging7080147

SparseAlign: A grid-free algorithm for automatic marker localization and deformation estimation in cryo-electron tomography

Author(s): P.S. Ganguly, F. Lucka, H. Kohr, E. Franken, H.J. Hupkes, K.J. Batenburg
Published in: IEEE Transactions on Computational Imaging, 23339403, 2022, Page(s) 651-665, ISSN 2333-9403
Publisher: IEEE
DOI: 10.1109/tci.2022.3194719

PCA reduced Gaussian mixture models with applications in superresolution

Author(s): Johannes Hertrich, Dang-Phuong-Lan Nguyen, Jean-Francois Aujol, Dominique Bernard, Yannick Berthoumieu, Abdellatif Saadaldin, Gabriele Steidl
Published in: Inverse Problems & Imaging, 0/0, 2021, ISSN 1930-8337
Publisher: American Institute of Mathematical Sciences
DOI: 10.3934/ipi.2021053

Tomographic Reconstruction of the Small-Angle X-Ray Scattering Tensor with Filtered Back Projection

Author(s): Jisoo Kim; Daniël M. Pelt; Matias Kagias; Marco Stampanoni; K. Joost Batenburg; Federica Marone
Published in: Physical Review Applied, 23317019, 2022, ISSN 2331-7019
Publisher: American Physical Society
DOI: 10.1103/physrevapplied.18.014043

X-ray tomography based numerical analysis of stress concentrations in non-crimp fabric reinforced composites - assessment of segmentation methods

Author(s): R M Auenhammer, L P Mikkelsen, L E Asp, B J Blinzler
Published in: IOP Conference Series: Materials Science and Engineering, 942, 2020, Page(s) 012038, ISSN 1757-899X
Publisher: IOP Conference Series: Materials Science and Engineering
DOI: 10.1088/1757-899x/942/1/012038

Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabric reinforced composites

Author(s): Robert M. Auenhammer; Robert M. Auenhammer; Lars Pilgaard Mikkelsen; Leif Asp; Brina J. Blinzler
Published in: Auenhammer , R M , Mikkelsen , L P , Asp , L E & Blinzler , B J 2021 , ' Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabric reinforced composites ' , Composite Structures , vol. 256 , 113136 . https://doi.org/10.1016/j.compstruct.2020.113136, 1, 2020, ISSN 0263-8223
Publisher: Elsevier BV
DOI: 10.1016/j.compstruct.2020.113136

Conference proceedings (8)

Atomic Super-Resolution Tomography

Author(s): P.S. Ganguly, F. Lucka, H.J. Hupkes, K.J. Batenburg
Published in: Combinatorial Image Analysis, 20th International Workshop, IWCIA 2020, Novi Sad, Serbia, July 16–18, 2020, Lecture Notes in Computer Science Vol.12148, 2020, Page(s) 45-61, ISBN 978-3-030-51002-2
Publisher: Springer
DOI: 10.1007/978-3-030-51002-2

A Tomographic Reconstruction Method using Coordinate-based Neural Network with Spatial Regularization

Author(s): Jakeoung Koo, Elise Otterlei Brenne, Anders Bjorholm Dahl, Vedrana Andersen Dahl
Published in: Proceedings of the Northern Lights Deep Learning Workshop 2021, 2021
Publisher: Septentrio Academic Publishing
DOI: 10.7557/18.5676

Cloud enabling educational platforms with corc

Author(s): Rasmus Munk, David Marchant and Brian Vinter
Published in: Proceedings of the 8th Workshop on Cloud Technologies in Education (CTE2020), 2020
Publisher: Proceedings of the 8th Workshop on Cloud Technologies in Education (CTE2020)

The significance of the spectral correction of photon counting detector response in material classification from spectral x-ray CT

Author(s): Doniyor Jumanazarov, Ja-Keoung Koo, Henning F. Poulsen, Ulrik L. Olsen, Mihai Iovea
Published in: Quantum Optics and Photon Counting 2021, 1, 2021, Page(s) 15, ISBN 9781510643772
Publisher: SPIE
DOI: 10.1117/12.2589290

Abstract 'Deep learning based missing wedge artefact removal for electron tomography'

Author(s): J. Rimpeläinen, S. Bazrafkan, J. Sijbers, J. De Beenhouwer
Published in: (2019) MC 2019 Berlin Microscopy Conference - Abstracts. Regensburg - IM7.004, 2019, Page(s) 660-661
Publisher: Deutsche Gesellschaft fur elektronenmikroskopie

Managing Event Oriented Workflows

Author(s): David Marchant, Rasmus Munk, Elise O. Brenne, Brian Vinter
Published in: 2020 IEEE/ACM 2nd Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP), 2020, Page(s) 23-28, ISBN 978-1-6654-2282-6
Publisher: IEEE
DOI: 10.1109/xloop51963.2020.00009

From instrument to publication: A First Attempt at an Integrated Cloud for X-ray Facilities

Author(s): Munk, Rasmus; Brian Vinter; Zdenek Matej; Artur Barczyk
Published in: Book of Abstracts of Cloud Services for Synchronisation and Sharing (CS3) 2020 - the 6th Cloud Synchronization & Sharing Conference, 2020
Publisher: Cloud Services for Synchronisation and Sharing (CS3)

Teaching Concurrent and Distributed Programming With Concepts Over Mathematical Proofs

Author(s): David Marchant, Carl-Johannes Johnsen, Brian Vinter, Kenneth Skovhede
Published in: 2019 IEEE/ACM Workshop on Education for High-Performance Computing (EduHPC), 2019, Page(s) 49-57, ISBN 978-1-7281-5975-1
Publisher: IEEE
DOI: 10.1109/eduhpc49559.2019.00012