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Register a new userLimited Angle Tomography for Transmission X-Ray Microscopy Using Deep Learning
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In transmission X-ray microscopy (TXM) systems, the rotation of a scanned sample might be restricted to a limited angular range to avoid collision to other system parts or high attenuation at certain tilting angles. Image reconstruction from such limited angle data suffers from artifacts due to missing data. In this work, deep learning is applied to limited angle reconstruction in TXMs for the first time. With the challenge to obtain sufficient real data for training, training a deep neural network from synthetic data is investigated. Particularly, the U-Net, the state-of-the-art neural network in biomedical imaging, is trained from synthetic ellipsoid data and multi-category data to reduce artifacts in filtered back-projection (FBP) reconstruction images. The proposed method is evaluated on synthetic data and real scanned chlorella data in $100^circ$ limited angle tomography. For synthetic test data, the U-Net significantly reduces root-mean-square error (RMSE) from $2.55 times 10^{-3}$ {mu}m$^{-1}$ in the FBP reconstruction to $1.21 times 10^{-3}$ {mu}m$^{-1}$ in the U-Net reconstruction, and also improves structural similarity (SSIM) index from 0.625 to 0.920. With penalized weighted least square denoising of measured projections, the RMSE and SSIM are further improved to $1.16 times 10^{-3}$ {mu}m$^{-1}$ and 0.932, respectively. For real test data, the proposed method remarkably improves the 3-D visualization of the subcellular structures in the chlorella cell, which indicates its important value for nano-scale imaging in biology, nanoscience and materials science.
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Robustness of deep learning methods for limited angle tomography is challenged by two major factors: a) due to insufficient training data the network may not generalize well to unseen data; b) deep learning methods are sensitive to noise. Thus, generating reconstructed images directly from a neural network appears inadequate. We propose to constrain the reconstructed images to be consistent with the measured projection data, while the unmeasured information is complemented by learning based methods. For this purpose, a data consistent artifact reduction (DCAR) method is introduced: First, a prior image is generated from an initial limited angle reconstruction via deep learning as a substitute for missing information. Afterwards, a conventional iterative reconstruction algorithm is applied, integrating the data consistency in the measured angular range and the prior information in the missing angular range. This ensures data integrity in the measured area, while inaccuracies incorporated by the deep learning prior lie only in areas where no information is acquired. The proposed DCAR method achieves significant image quality improvement: for 120-degree cone-beam limited angle tomography more than 10% RMSE reduction in noise-free case and more than 24% RMSE reduction in noisy case compared with a state-of-the-art U-Net based method.
Low dose computed tomography (LDCT) is desirable for both diagnostic imaging and image guided interventions. Denoisers are openly used to improve the quality of LDCT. Deep learning (DL)-based denoisers have shown state-of-the-art performance and are becoming one of the mainstream methods. However, there exists two challenges regarding the DL-based denoisers: 1) a trained model typically does not generate different image candidates with different noise-resolution tradeoffs which sometimes are needed for different clinical tasks; 2) the model generalizability might be an issue when the noise level in the testing images is different from that in the training dataset. To address these two challenges, in this work, we introduce a lightweight optimization process at the testing phase on top of any existing DL-based denoisers to generate multiple image candidates with different noise-resolution tradeoffs suitable for different clinical tasks in real-time. Consequently, our method allows the users to interact with the denoiser to efficiently review various image candidates and quickly pick up the desired one, and thereby was termed as deep interactive denoiser (DID). Experimental results demonstrated that DID can deliver multiple image candidates with different noise-resolution tradeoffs, and shows great generalizability regarding various network architectures, as well as training and testing datasets with various noise levels.
Limited-angle tomography of strongly scattering quasi-transparent objects is a challenging, highly ill-posed problem with practical implications in medical and biological imaging, manufacturing, automation, and environmental and food security. Regularizing priors are necessary to reduce artifacts by improving the condition of such problems. Recently, it was shown that one effective way to learn the priors for strongly scattering yet highly structured 3D objects, e.g. layered and Manhattan, is by a static neural network [Goy et al, Proc. Natl. Acad. Sci. 116, 19848-19856 (2019)]. Here, we present a radically different approach where the collection of raw images from multiple angles is viewed analogously to a dynamical system driven by the object-dependent forward scattering operator. The sequence index in angle of illumination plays the role of discrete time in the dynamical system analogy. Thus, the imaging problem turns into a problem of nonlinear system identification, which also suggests dynamical learning as better fit to regularize the reconstructions. We devised a recurrent neural network (RNN) architecture with a novel split-convolutional gated recurrent unit (SC-GRU) as the fundamental building block. Through comprehensive comparison of several quantitative metrics, we show that the dynamic method improves upon previous static approaches with fewer artifacts and better overall reconstruction fidelity.
Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique in biomedical research that uses the fluorophore decay rate to provide additional contrast in fluorescence microscopy. However, at present, the calculation, analysis, and interpretation of FLIM is a complex, slow, and computationally expensive process. Machine learning (ML) techniques are well suited to extract and interpret measurements from multi-dimensional FLIM data sets with substantial improvement in speed over conventional methods. In this topical review, we first discuss the basics of FILM and ML. Second, we provide a summary of lifetime extraction strategies using ML and its applications in classifying and segmenting FILM images with higher accuracy compared to conventional methods. Finally, we discuss two potential directions to improve FLIM with ML with proof of concept demonstrations.
The development of personalized human head models from medical images has become an important topic in the electromagnetic dosimetry field, including the optimization of electrostimulation, safety assessments, etc. Human head models are commonly generated via the segmentation of magnetic resonance images into different anatomical tissues. This process is time consuming and requires special experience for segmenting a relatively large number of tissues. Thus, it is challenging to accurately compute the electric field in different specific brain regions. Recently, deep learning has been applied for the segmentation of the human brain. However, most studies have focused on the segmentation of brain tissue only and little attention has been paid to other tissues, which are considerably important for electromagnetic dosimetry. In this study, we propose a new architecture for a convolutional neural network, named ForkNet, to perform the segmentation of whole human head structures, which is essential for evaluating the electrical field distribution in the brain. The proposed network can be used to generate personalized head models and applied for the evaluation of the electric field in the brain during transcranial magnetic stimulation. Our computational results indicate that the head models generated using the proposed network exhibit strong matching with those created via manual segmentation in an intra-scanner segmentation task.
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