Machine Learning Methods for Brain Image Analysis

Understanding how the brain functions and quantifying compound interactions between complex synaptic networks inside the brain remain some of the most challenging problems in neuroscience. Lack or abundance of data, shortage of manpower along with heterogeneity of data following from various species all served as an added complexity to the already perplexing problem. The ability to process vast amount of brain data need to be performed automatically, yet with an accuracy close to manual human-level performance. These automated methods essentially need to generalize well to be able to accommodate data from different species. Also, novel approaches and techniques are becoming a necessity to reveal the correlations between different data modalities in the brain at the global level. In this dissertation, I mainly focus on two problems: automatic segmentation of brain electron microscopy (EM) images and stacks, and integrative analysis of the gene expression and synaptic connectivity in the brain. I propose to use deep learning algorithms for the 2D segmentation of EM images. I designed an automated pipeline with novel insights that was able to achieve state-of-the-art performance on the segmentation of the \textit{Drosophila} brain. I also propose a novel technique for 3D segmentation of EM image stacks that can be trained end-to-end with no prior knowledge of the data. This technique was evaluated in an ongoing online challenge for 3D segmentation of neurites where it achieved accuracy close to a second human observer. Later, I employed ensemble learning methods to perform the first systematic integrative analysis of the genome and connectome in the mouse brain at both the regional- and voxel-level. I show that the connectivity signals can be predicted from the gene expression signatures with an extremely high accuracy. Furthermore, I show that only a certain fraction of genes are responsible for this predictive aspect. Rich functional and cellular analysis of these genes are detailed to validate these findings

Cross-Calibration of S-NPP VIIRS Moderate Resolution Reflective Solar Bands Against MODIS Aqua over Dark Water Scenes

The Visible Infrared Imaging Radiometer Suite (VIIRS) is being used to continue the record of Earth Science observations and data products produced routinely from National Aeronautics and Space Administration (NASA) Moderate Resolution Imaging Spectroradiometer (MODIS) measurements. However, the absolute calibration of VIIRS's reflected solar bands is thought to be biased, leading to offsets in derived data products such as aerosol optical depth (AOD) as compared to when similar algorithms are applied to different sensors. This study presents a cross-calibration of these VIIRS bands against MODIS Aqua over dark water scenes, finding corrections to the NASA VIIRS Level 1 (version 2) reflectances between approximately +1 and 7 % (dependent on band) are needed to bring the two into alignment (after accounting for expected differences resulting from different band spectral response functions), and indications of relative trending of up to 0.35 % per year in some bands. The derived calibration gain corrections are also applied to the VIIRS reflectance and then used in an AOD retrieval, and they are shown to decrease the bias and total error in AOD across the mid-visible spectral region compared to the standard VIIRS NASA reflectance calibration. The resulting AOD bias characteristics are similar to those of NASA MODIS AOD data products, which is encouraging in terms of multi-sensor data continuity

ExoGAN: Retrieving Exoplanetary Atmospheres Using Deep Convolutional Generative Adversarial Networks

Atmospheric retrievals on exoplanets usually involve computationally intensive Bayesian sampling methods. Large parameter spaces and increasingly complex atmospheric models create a computational bottleneck forcing a trade-off between statistical sampling accuracy and model complexity. It is especially true for upcoming JWST and ARIEL observations. We introduce ExoGAN, the Exoplanet Generative Adversarial Network, a new deep learning algorithm able to recognise molecular features, atmospheric trace-gas abundances and planetary parameters using unsupervised learning. Once trained, ExoGAN is widely applicable to a large number of instruments and planetary types. The ExoGAN retrievals constitute a significant speed improvement over traditional retrievals and can be used either as a final atmospheric analysis or provide prior constraints to subsequent retrieval.Comment: 19 pages, 17 figures, 7 table

Advanced Sensing, Fault Diagnostics, and Structural Health Management

Advanced sensing, fault diagnosis, and structural health management are important parts of the maintenance strategy of modern industries. With the advancement of science and technology, modern structural and mechanical systems are becoming more and more complex. Due to the continuous nature of operation and utilization, modern systems are heavily susceptible to faults. Hence, the operational reliability and safety of the systems can be greatly enhanced by using the multifaced strategy of designing novel sensing technologies and advanced intelligent algorithms and constructing modern data acquisition systems and structural health monitoring techniques. As a result, this research domain has been receiving a significant amount of attention from researchers in recent years. Furthermore, the research findings have been successfully applied in a wide range of fields such as aerospace, manufacturing, transportation and processes

Recent Advances in Forensic Anthropological Methods and Research

Forensic anthropology, while still relatively in its infancy compared to other forensic science disciplines, adopts a wide array of methods from many disciplines for human skeletal identification in medico-legal and humanitarian contexts. The human skeleton is a dynamic tissue that can withstand the ravages of time given the right environment and may be the only remaining evidence left in a forensic case whether a week or decades old. Improved understanding of the intrinsic and extrinsic factors that modulate skeletal tissues allows researchers and practitioners to improve the accuracy and precision of identification methods ranging from establishing a biological profile such as estimating age-at-death, and population affinity, estimating time-since-death, using isotopes for geolocation of unidentified decedents, radiology for personal identification, histology to assess a live birth, to assessing traumatic injuries and so much more

Automatic image analysis of C-arm Computed Tomography images for ankle joint surgeries

Open reduction and internal fixation is a standard procedure in ankle surgery for treating a fractured fibula. Since fibula fractures are often accompanied by an injury of the syndesmosis complex, it is essential to restore the correct relative pose of the fibula relative to the adjoining tibia for the ligaments to heal. Otherwise, the patient might experience instability of the ankle leading to arthritis and ankle pain and ultimately revision surgery. Incorrect positioning referred to as malreduction of the fibula is assumed to be one of the major causes of unsuccessful ankle surgery. 3D C-arm imaging is the current standard procedure for revealing malreduction of fractures in the operating room. However, intra-operative visual inspection of the reduction result is complicated due to high inter-individual variation of the ankle anatomy and rather based on the subjective experience of the surgeon. A contralateral side comparison with the patient’s uninjured ankle is recommended but has not been integrated into clinical routine due to the high level of radiation exposure it incurs. This thesis presents the first approach towards a computer-assisted intra-operative contralateral side comparison of the ankle joint. The focus of this thesis was the design, development and validation of a software-based prototype for a fully automatic intra-operative assistance system for orthopedic surgeons. The implementation does not require an additional 3D C-arm scan of the uninjured ankle, thus reducing time consumption and cumulative radiation dose. A 3D statistical shape model (SSM) is used to reconstruct a 3D surface model from three 2D fluoroscopic projections representing the uninjured ankle. To this end, a 3D SSM segmentation is performed on the 3D image of the injured ankle to gain prior knowledge of the ankle. A 3D convolutional neural network (CNN) based initialization method was developed and its outcome was incorporated into the SSM adaption step. Segmentation quality was shown to be improved in terms of accuracy and robustness compared to the pure intensity-based SSM. This allows us to overcome the limitations of the previously proposed methods, namely inaccuracy due to metal artifacts and the lack of device-to-patient orientation of the C-arm. A 2D-CNN is employed to extract semantic knowledge from all fluoroscopic projection images. This step of the pipeline both creates features for the subsequent reconstruction and also helps to pre-initialize the 3D-SSM without user interaction. A 2D-3D multi-bone reconstruction method has been developed which uses distance maps of the 2D features for fast and accurate correspondence optimization and SSM adaption. This is the central and most crucial component of the workflow. This is the first time that a bone reconstruction method has been applied to the complex ankle joint and the first reconstruction method using CNN based segmentations as features. The reconstructed 3D-SSM of the uninjured ankle can be back-projected and visualized in a workflow-oriented manner to procure clear visualization of the region of interest, which is essential for the evaluation of the reduction result. The surgeon can thus directly compare an overlay of the contralateral ankle with the injured ankle. The developed methods were evaluated individually using data sets acquired during a cadaver study and representative clinical data acquired during fibular reduction. A hierarchical evaluation was designed to assess the inaccuracies of the system on different levels and to identify major sources of error. The overall evaluation performed on eleven challenging clinical datasets acquired for manual contralateral side comparison showed that the system is capable of accurately reconstructing 3D surface models of the uninjured ankle solely using three projection images. A mean Hausdorff distance of 1.72 mm was measured when comparing the reconstruction result to the ground truth segmentation and almost achieved the high required clinical accuracy of 1-2 mm. The overall error of the pipeline was mainly attributed to inaccuracies in the 2D-CNN segmentation. The consistency of these results requires further validation on a larger dataset. The workflow proposed in this thesis establishes the first approach to enable automatic computer-assisted contralateral side comparison in ankle surgery. The feasibility of the proposed approach was proven on a limited amount of clinical cases and has already yielded good results. The next important step is to alleviate the identified bottlenecks in the approach by providing more training data in order to further improve the accuracy. In conclusion, the new approach presented gives the chance to guide the surgeon during the reduction process, improve the surgical outcome while avoiding additional radiation exposure and reduce the number of revision surgeries in the long term