Search Results for author: Mareike Thies

Found 22 papers, 6 papers with code

Reference-Free Multi-Modality Volume Registration of X-Ray Microscopy and Light-Sheet Fluorescence Microscopy

no code implementations23 Apr 2024 Siyuan Mei, Fuxin Fan, Mareike Thies, Mingxuan Gu, Fabian Wagner, Oliver Aust, Ina Erceg, Zeynab Mirzaei, Georgiana Neag, Yipeng Sun, Yixing Huang, Andreas Maier

Recently, X-ray microscopy (XRM) and light-sheet fluorescence microscopy (LSFM) have emerged as two pivotal imaging tools in preclinical research on bone remodeling diseases, offering micrometer-level resolution.

Physics-Informed Learning for Time-Resolved Angiographic Contrast Agent Concentration Reconstruction

no code implementations4 Mar 2024 Noah Maul, Annette Birkhold, Fabian Wagner, Mareike Thies, Maximilian Rohleder, Philipp Berg, Markus Kowarschik, Andreas Maier

In our work, we implicitly include this information in a neural network-based model that is trained on a dataset of image-based blood flow simulations.

Anatomy

Data-Driven Filter Design in FBP: Transforming CT Reconstruction with Trainable Fourier Series

1 code implementation29 Jan 2024 Yipeng Sun, Linda-Sophie Schneider, Fuxin Fan, Mareike Thies, Mingxuan Gu, Siyuan Mei, Yuzhong Zhou, Siming Bayer, Andreas Maier

In this study, we introduce a Fourier series-based trainable filter for computed tomography (CT) reconstruction within the filtered backprojection (FBP) framework.

Computational Efficiency Computed Tomography (CT)

Exploring Epipolar Consistency Conditions for Rigid Motion Compensation in In-vivo X-ray Microscopy

no code implementations1 Mar 2023 Mareike Thies, Fabian Wagner, Mingxuan Gu, Siyuan Mei, Yixing Huang, Sabrina Pechmann, Oliver Aust, Daniela Weidner, Georgiana Neag, Stefan Uderhardt, Georg Schett, Silke Christiansen, Andreas Maier

Intravital X-ray microscopy (XRM) in preclinical mouse models is of vital importance for the identification of microscopic structural pathological changes in the bone which are characteristic of osteoporosis.

Motion Compensation

Geometric Constraints Enable Self-Supervised Sinogram Inpainting in Sparse-View Tomography

no code implementations13 Feb 2023 Fabian Wagner, Mareike Thies, Noah Maul, Laura Pfaff, Oliver Aust, Sabrina Pechmann, Christopher Syben, Andreas Maier

By reconstructing independent stacks of projection data, a self-supervised loss is calculated in the CT image domain and used to directly optimize projection image intensities to match the missing tomographic views constrained by the projection geometry.

Computed Tomography (CT) SSIM

Optimizing CT Scan Geometries With and Without Gradients

no code implementations13 Feb 2023 Mareike Thies, Fabian Wagner, Noah Maul, Laura Pfaff, Linda-Sophie Schneider, Christopher Syben, Andreas Maier

In computed tomography (CT), the projection geometry used for data acquisition needs to be known precisely to obtain a clear reconstructed image.

Computed Tomography (CT) Motion Compensation

On the Benefit of Dual-domain Denoising in a Self-supervised Low-dose CT Setting

1 code implementation2 Nov 2022 Fabian Wagner, Mareike Thies, Laura Pfaff, Oliver Aust, Sabrina Pechmann, Daniela Weidner, Noah Maul, Maximilian Rohleder, Mingxuan Gu, Jonas Utz, Felix Denzinger, Andreas Maier

In this work, we present an end-to-end trainable CT reconstruction pipeline that contains denoising operators in both the projection and the image domain and that are optimized simultaneously without requiring ground-truth high-dose CT data.

Computed Tomography (CT) Image Denoising +1

Trainable Joint Bilateral Filters for Enhanced Prediction Stability in Low-dose CT

no code implementations15 Jul 2022 Fabian Wagner, Mareike Thies, Felix Denzinger, Mingxuan Gu, Mayank Patwari, Stefan Ploner, Noah Maul, Laura Pfaff, Yixing Huang, Andreas Maier

Low-dose computed tomography (CT) denoising algorithms aim to enable reduced patient dose in routine CT acquisitions while maintaining high image quality.

Computed Tomography (CT) Denoising

ConFUDA: Contrastive Fewshot Unsupervised Domain Adaptation for Medical Image Segmentation

no code implementations8 Jun 2022 Mingxuan Gu, Sulaiman Vesal, Mareike Thies, Zhaoya Pan, Fabian Wagner, Mirabela Rusu, Andreas Maier, Ronak Kosti

Then, to align the source and target features and tackle the memory issue of the traditional contrastive loss, we propose the centroid-based contrastive learning (CCL) and a centroid norm regularizer (CNR) to optimize the contrastive pairs in both direction and magnitude.

Contrastive Learning Image Segmentation +4

Ultra Low-Parameter Denoising: Trainable Bilateral Filter Layers in Computed Tomography

1 code implementation25 Jan 2022 Fabian Wagner, Mareike Thies, Mingxuan Gu, Yixing Huang, Sabrina Pechmann, Mayank Patwari, Stefan Ploner, Oliver Aust, Stefan Uderhardt, Georg Schett, Silke Christiansen, Andreas Maier

Due to the extremely low number of trainable parameters with well-defined effect, prediction reliance and data integrity is guaranteed at any time in the proposed pipelines, in contrast to most other deep learning-based denoising architectures.

Denoising SSIM

Learned Cone-Beam CT Reconstruction Using Neural Ordinary Differential Equations

no code implementations19 Jan 2022 Mareike Thies, Fabian Wagner, Mingxuan Gu, Lukas Folle, Lina Felsner, Andreas Maier

Learned iterative reconstruction algorithms for inverse problems offer the flexibility to combine analytical knowledge about the problem with modules learned from data.

Numerical Integration

A Learning-based Method for Online Adjustment of C-arm Cone-Beam CT Source Trajectories for Artifact Avoidance

no code implementations14 Aug 2020 Mareike Thies, Jan-Nico Zäch, Cong Gao, Russell Taylor, Nassir Navab, Andreas Maier, Mathias Unberath

We propose to adjust the C-arm CBCT source trajectory during the scan to optimize reconstruction quality with respect to a certain task, i. e. verification of screw placement.

Anatomy Tomographic Reconstructions

A County-level Dataset for Informing the United States' Response to COVID-19

1 code implementation1 Apr 2020 Benjamin D. Killeen, Jie Ying Wu, Kinjal Shah, Anna Zapaishchykova, Philipp Nikutta, Aniruddha Tamhane, Shreya Chakraborty, Jinchi Wei, Tiger Gao, Mareike Thies, Mathias Unberath

As the coronavirus disease 2019 (COVID-19) becomes a global pandemic, policy makers must enact interventions to stop its spread.

Computers and Society Databases Physics and Society Populations and Evolution

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