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Register a new userAn Automated Images-to-Graphs Framework for High Resolution Connectomics
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Reconstructing a map of neuronal connectivity is a critical challenge in contemporary neuroscience. Recent advances in high-throughput serial section electron microscopy (EM) have produced massive 3D image volumes of nanoscale brain tissue for the first time. The resolution of EM allows for individual neurons and their synaptic connections to be directly observed. Recovering neuronal networks by manually tracing each neuronal process at this scale is unmanageable, and therefore researchers are developing automated image processing modules. Thus far, state-of-the-art algorithms focus only on the solution to a particular task (e.g., neuron segmentation or synapse identification). In this manuscript we present the first fully automated images-to-graphs pipeline (i.e., a pipeline that begins with an imaged volume of neural tissue and produces a brain graph without any human interaction). To evaluate overall performance and select the best parameters and methods, we also develop a metric to assess the quality of the output graphs. We evaluate a set of algorithms and parameters, searching possible operating points to identify the best available brain graph for our assessment metric. Finally, we deploy a reference end-to-end version of the pipeline on a large, publicly available data set. This provides a baseline result and framework for community analysis and future algorithm development and testing. All code and data derivatives have been made publicly available toward eventually unlocking new biofidelic computational primitives and understanding of neuropathologies.
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The field of connectomics faces unprecedented big data challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide relatively good accuracy but are unacceptably slow, and would require years to extract connectivity graphs from even a single cubic millimeter of neural tissue. Here we present a viable real-time solution, a multi-pass pipeline optimized for shared-memory multicore systems, capable of processing data at near the terabyte-per-hour pace of multi-beam electron microscopes. The pipeline makes an initial fast-pass over the data, and then makes a second slow-pass to iteratively correct errors in the output of the fast-pass. We demonstrate the accuracy of a sparse slow-pass reconstruction algorithm and suggest new methods for detecting morphological errors. Our fast-pass approach provided many algorithmic challenges, including the design and implementation of novel shallow convolutional neural nets and the parallelization of watershed and object-merging techniques. We use it to reconstruct, from image stack to skeletons, the full dataset of Kasthuri et al. (463 GB capturing 120,000 cubic microns) in a matter of hours on a single multicore machine rather than the weeks it has taken in the past on much larger distributed systems.
Quantification of myocardial perfusion has the potential to improve detection of regional and global flow reduction. Significant effort has been made to automate the workflow, where one essential step is the arterial input function (AIF) extraction. Since failure here invalidates quantification, high accuracy is required. For this purpose, this study presents a robust AIF detection method using the convolutional neural net (CNN) model. CNN models were trained by assembling 25,027 scans (N=12,984 patients) from three hospitals, seven scanners. A test set of 5,721 scans (N=2,805 patients) evaluated model performance. The 2D+T AIF time series was inputted into CNN. Two variations were investigated: a) Two Classes (2CS) for background and foreground (LV mask); b) Three Classes (3CS) for background, foreground LV and RV. Final model was deployed on MR scanners via the Gadgetron InlineAI. Model loading time on MR scanner was ~340ms and applying it took ~180ms. The 3CS model successfully detect LV for 99.98% of all test cases (1 failed out of 5,721 cases). The mean Dice ratio for 3CS was 0.87+/-0.08 with 92.0% of all test cases having Dice ratio >0.75, while the 2CS model gave lower Dice of 0.82+/-0.22 (P<1e-5). Extracted AIF signals using CNN were further compared to manual ground-truth for foot-time, peak-time, first-pass duration, peak value and area-under-curve. No significant differences were found for all features (P>0.2). This study proposed, validated, and deployed a robust CNN solution to detect the LV for the extraction of the AIF signal used in fully automated perfusion flow mapping. A very large data cohort was assembled and resulting models were deployed to MR scanners for fully inline AI in clinical hospitals.
Like many scientific fields, new chemistry literature has grown at a staggering pace, with thousands of papers released every month. A large portion of chemistry literature focuses on new molecules and reactions between molecules. Most vital information is conveyed through 2-D images of molecules, representing the underlying molecules or reactions described. In order to ensure reproducible and machine-readable molecule representations, text-based molecule descriptors like SMILES and SELFIES were created. These text-based molecule representations provide molecule generation but are unfortunately rarely present in published literature. In the absence of molecule descriptors, the generation of molecule descriptors from the 2-D images present in the literature is necessary to understand chemistry literature at scale. Successful methods such as Optical Structure Recognition Application (OSRA), and ChemSchematicResolver are able to extract the locations of molecules structures in chemistry papers and infer molecular descriptions and reactions. While effective, existing systems expect chemists to correct outputs, making them unsuitable for unsupervised large-scale data mining. Leveraging the task formulation of image captioning introduced by DECIMER, we introduce IMG2SMI, a model which leverages Deep Residual Networks for image feature extraction and an encoder-decoder Transformer layers for molecule description generation. Unlike previous Neural Network-based systems, IMG2SMI builds around the task of molecule description generation, which enables IMG2SMI to outperform OSRA-based systems by 163% in molecule similarity prediction as measured by the molecular MACCS Fingerprint Tanimoto Similarity. Additionally, to facilitate further research on this task, we release a new molecule prediction dataset. including 81 million molecules for molecule description generation
Recent development of quantitative myocardial blood flow (MBF) mapping allows direct evaluation of absolute myocardial perfusion, by computing pixel-wise flow maps. Clinical studies suggest quantitative evaluation would be more desirable for objectivity and efficiency. Objective assessment can be further facilitated by segmenting the myocardium and automatically generating reports following the AHA model. This will free user interaction for analysis and lead to a one-click solution to improve workflow. This paper proposes a deep neural network based computational workflow for inline myocardial perfusion analysis. Adenosine stress and rest perfusion scans were acquired from three hospitals. Training set included N=1,825 perfusion series from 1,034 patients. Independent test set included 200 scans from 105 patients. Data were consecutively acquired at each site. A convolution neural net (CNN) model was trained to provide segmentation for LV cavity, myocardium and right ventricular by processing incoming 2D+T perfusion Gd series. Model outputs were compared to manual ground-truth for accuracy of segmentation and flow measures derived on global and per-sector basis. The trained models were integrated onto MR scanners for effective inference. Segmentation accuracy and myocardial flow measures were compared between CNN models and manual ground-truth. The mean Dice ratio of CNN derived myocardium was 0.93 +/- 0.04. Both global flow and per-sector values showed no significant difference, compared to manual results. The AHA 16 segment model was automatically generated and reported on the MR scanner. As a result, the fully automated analysis of perfusion flow mapping was achieved. This solution was integrated on the MR scanner, enabling one-click analysis and reporting of myocardial blood flow.
Modeling biological rhythms helps understand the complex principles behind the physical and psychological abnormalities of human bodies, to plan life schedules, and avoid persisting fatigue and mood and sleep alterations due to the desynchronization of those rhythms. The first step in modeling biological rhythms is to identify their characteristics, such as cyclic periods, phase, and amplitude. However, human rhythms are susceptible to external events, which cause irregular fluctuations in waveforms and affect the characterization of each rhythm. In this paper, we present our exploratory work towards developing a computational framework for automated discovery and modeling of human rhythms. We first identify cyclic periods in time series data using three different methods and test their performance on both synthetic data and real fine-grained biological data. We observe consistent periods are detected by all three methods. We then model inner cycles within each period through identifying change points to observe fluctuations in biological data that may inform the impact of external events on human rhythms. The results provide initial insights into the design of a computational framework for discovering and modeling human rhythms.
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