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Register a new userIndependent Component Analysis for noise and artifact removal in Three-dimensional Polarized Light Imaging
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Authors
Kai Benning
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In recent years, Independent Component Analysis (ICA) has successfully been applied to remove noise and artifacts in images obtained from Three-dimensional Polarized Light Imaging (3D-PLI) at the mesoscale (i.e., 64 $mu$m). Here, we present an automatic denoising procedure for gray matter regions that allows to apply the ICA also to microscopic images, with reasonable computational effort. Apart from an automatic segmentation of gray matter regions, we applied the denoising procedure to several 3D-PLI images from a rat and a vervet monkey brain section.
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Novel methods for quantitative, transient-state multiparametric imaging are increasingly being demonstrated for assessment of disease and treatment efficacy. Here, we build on these by assessing the most common Non-Cartesian readout trajectories (2D/3D radials and spirals), demonstrating efficient anti-aliasing with a k-space view-sharing technique, and proposing novel methods for parameter inference with neural networks that incorporate the estimation of proton density. Our results show good agreement with gold standard and phantom references for all readout trajectories at 1.5T and 3T. Parameters inferred with the neural network were within 6.58% difference from the parameters inferred with a high-resolution dictionary. Concordance correlation coefficients were above 0.92 and the normalized root mean squared error ranged between 4.2% - 12.7% with respect to gold-standard phantom references for T1 and T2. In vivo acquisitions demonstrate sub-millimetric isotropic resolution in under five minutes with reconstruction and inference times < 7 minutes. Our 3D quantitative transient-state imaging approach could enable high-resolution multiparametric tissue quantification within clinically acceptable acquisition and reconstruction times.
Purpose: Using 4D magnetic particle imaging (MPI), intravascular optical coherence tomography (IVOCT) catheters are tracked in real time in order to compensate for image artifacts related to relative motion. Our approach demonstrates the feasibility for bimodal IVOCT and MPI in-vitro experiments. Material and Methods: During IVOCT imaging of a stenosis phantom the catheter is tracked using MPI. A 4D trajectory of the catheter tip is determined from the MPI data using center of mass sub-voxel strategies. A custom built IVOCT imaging adapter is used to perform different catheter motion profiles: no motion artifacts, motion artifacts due to catheter bending, and heart beat motion artifacts. Two IVOCT volume reconstruction methods are compared qualitatively and quantitatively using the DICE metric and the known stenosis length. Results: The MPI-tracked trajectory of the IVOCT catheter is validated in multiple repeated measurements calculating the absolute mean error and standard deviation. Both volume reconstruction methods are compared and analyzed whether they are capable of compensating the motion artifacts. The novel approach of MPI-guided catheter tracking corrects motion artifacts leading to a DICE coefficient with a minimum of 86% in comparison to 58% for a standard reconstruction approach. Conclusions: IVOCT catheter tracking with MPI in real time is an auspicious method for radiation free MPI-guided IVOCT interventions. The combination of MPI and IVOCT can help to reduce motion artifacts due to catheter bending and heart beat for optimized IVOCT volume reconstructions.
Fluorine-19 (19F) MRI of injected perfluorocarbon emulsions (PFCs) allows for the non-invasive quantification of inflammation and cell tracking, but suffers from a low signal-to-noise ratio and extended scan time. To address this limitation, we tested the hypothesis that a 19F MRI pulse sequence that combines a specific undersampling regime with signal averaging has increased sensitivity and robustness against motion artifacts compared to a non-averaged fully-sampled dataset, when both are reconstructed with compressed sensing. To this end, numerical simulations and phantom experiments were performed to characterize the point spread function (PSF) of undersampling patterns and the vulnerability to noise of acquisition-reconstruction strategies with paired numbers of x signal averages and acceleration factor x (NAx-AFx). At all investigated noise levels, the DSC of the acquisition-reconstruction strategies strongly depended on the regularization parameters and acceleration factor. In phantoms, motion robustness of an NA8-AF8 undersampling pattern versus NA1-AF1 was evaluated with simulated and real motions. Differences were assessed with Dice similarity coefficients (DSC), and were consistently higher for NA8-AF8 compared to NA1-AF1 strategy, for both simulated and real cyclic motions (P<0.001). Both acquisition-reconstruction strategies were validated in vivo in mice (n=2) injected with perfluoropolyether. These images displayed a sharper delineation of the liver with the NA8-AF8 strategy than with the NA1-AF1 strategy. In conclusion, we validated the hypothesis that in 19F MRI, the combination of undersampling and averaging improves both the sensitivity and the robustness against motion artifacts compared to a non-averaged fully-sampled dataset, when both are reconstructed with compressed sensing.
Recent works have demonstrated the added value of dynamic amino acid positron emission tomography (PET) for glioma grading and genotyping, biopsy targeting, and recurrence diagnosis. However, most of these studies are exclusively based on hand-crafted qualitative or semi-quantitative dynamic features extracted from the mean time activity curve (TAC) within predefined volumes. Voxelwise dynamic PET data analysis could instead provide a better insight into intra-tumour heterogeneity of gliomas. In this work, we investigate the ability of the widely used principal component analysis (PCA) method to extract meaningful quantitative dynamic features from high-dimensional motion-corrected dynamic [S-methyl-11C]methionine PET data in a first cohort of 20 glioma patients. By means of realistic numerical simulations, we demonstrate the robustness of our methodology to noise. In a second cohort of 13 glioma patients, we compare the resulting parametric maps to these provided by standard one- and two-tissue compartment pharmacokinetic (PK) models. We show that our PCA model outperforms PK models in the identification of intra-tumour uptake dynamics heterogeneity while being much less computationally expensive. Such parametric maps could be valuable to assess tumour aggressiveness locally with applications in treatment planning as well as in the evaluation of tumour progression and response to treatment. This work also provides further encouraging results on the added value of dynamic over static analysis of [S-methyl-11C]methionine PET data in gliomas, as previously demonstrated for O-(2-[18F]fluoroethyl)-L-tyrosine.
In this paper, we propose a new method for impulse noise removal from images. It uses the sparsity of images in the Discrete Cosine Transform (DCT) domain. The zeros in this domain give us the exact mathematical equation to reconstruct the pixels that are corrupted by random-value impulse noises. The proposed method can also detect and correct the corrupted pixels. Moreover, in a simpler case that salt and pepper noise is the brightest and darkest pixels in the image, we propose a simpler version of our method. In addition to the proposed method, we suggest a combination of the traditional median filter method with our method to yield better results when the percentage of the corrupted samples is high.
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