Yanhui Liang

Liver whole slide image analysis for 3D vessel reconstruction

The emergence of digital pathology has enabled numerous quantitative analyses of histopathology structures. However, most pathology image analyses are limited to two-dimensional datasets, resulting in substantial information loss and incomplete interpretation. To address this, we have developed a complete framework for three-dimensional whole slide image analysis and demonstrated its efficacy on 3D vessel structure analysis with liver tissue sections. The proposed workflow includes components on image registration, vessel segmentation, vessel cross-section association, object interpolation, and volumetric rendering. For 3D vessel reconstruction, a cost function is formulated based on shape descriptors, spatial similarity and trajectory smoothness by taking into account four vessel association scenarios. An efficient entropy-based Relaxed Integer Programming (eRIP) method is proposed to identify the optimal inter-frame vessel associations. The reconstructed 3D vessels are both quantitatively and qualitatively validated. Evaluation results demonstrate high efficiency and accuracy of the proposed method, suggesting its promise to support further 3D vessel analysis with whole slide images.

A framework for 3D vessel analysis using whole slide images of liver tissue sections

Three-dimensional (3D) high resolution microscopic images have high potential for improving the understanding of both normal and disease processes where structural changes or spatial relationship of disease features are significant. In this paper, we develop a complete framework applicable to 3D pathology analytical imaging, with an application to whole slide images of sequential liver slices for 3D vessel structure analysis. The analysis workflow consists of image registration, segmentation, vessel cross-section association, interpolation, and volumetric rendering. To identify biologically-meaningful correspondence across adjacent slides, we formulate a similarity function for four association cases. The optimal solution is then obtained by constrained Integer Programming. We quantitatively and qualitatively compare our vessel reconstruction results with human annotations. Validation results indicate a satisfactory concordance as measured both by region-based and distance-based metrics. These results demonstrate a promising 3D vessel analysis framework for whole slide images of liver tissue sections.

A 3D Primary Vessel Reconstruction Framework with Serial Microscopy Images

Three dimensional microscopy images present significant potential to enhance biomedical studies. This paper presents an automated method for quantitative analysis of 3D primary vessel structures with histology whole slide images. With registered microscopy images of liver tissue, we identify primary vessels with an improved variational level set framework at each 2D slide. We propose a Vessel Directed Fitting Energy (VDFE) to provide prior information on vessel wall probability in an energy minimization paradigm. We find the optimal vessel cross-section associations along the image sequence with a two-stage procedure. Vessel mappings are first found between each pair of adjacent slides with a similarity function for four association cases. These bi-slide vessel components are further linked by Bayesian Maximum A Posteriori (MAP) estimation where the posterior probability is modeled as a Markov chain. The efficacy of the proposed method is demonstrated with 54 whole slide microscopy images of sequential sections from a human liver.

Automated cell segmentation with 3D fluorescence microscopy images

A large number of cell-oriented cancer investigations require an effective and reliable cell segmentation method on three dimensional (3D) fluorescence microscopic images for quantitative analysis of cell biological properties. In this paper, we present a fully automated cell segmentation method that can detect cells from 3D fluorescence microscopic images. Enlightened by fluorescence imaging techniques, we regulated the image gradient field by gradient vector flow (GVF) with interpolated and smoothed data volume, and grouped voxels based on gradient modes identified by tracking GVF field. Adaptive thresholding was then applied to voxels associated with the same gradient mode where voxel intensities were enhanced by a multiscale cell filter. We applied the method to a large volume of 3D fluorescence imaging data of human brain tumor cells with (1) small cell false detection and missing rates for individual cells; and (2) trivial over and under segmentation incidences for clustered cells. Additionally, the concordance of cell morphometry structure between automated and manual segmentation was encouraging. These results suggest a promising 3D cell segmentation method applicable to cancer studies.

Parallel Processing over Spatial-Temporal Datasets from Geo, Bio, Climate and Social Science Communities: A Research Roadmap

This vision paper reviews the current state-ofart and lays out emerging research challenges in parallel processing of spatial-temporal large datasets relevant to a variety of scientific communities. The spatio-temporal data, whether captured through remote sensors (global earth observations), ground and ocean sensors (e.g., soil moisture sensors, buoys), social media and hand-held, traffic-related sensors and cameras, medical imaging (e.g., MRI), or large scale simulations (e.g., climate) have always been “big.” A common thread among all these big collections of datasets is that they are spatial and temporal. Processing and analyzing these datasets requires high-performance computing (HPC) infrastructures. Various agencies, scientific communities and increasingly the society at large rely on spatial data management, analysis, and spatial data mining to gain insights and produce actionable plans. Therefore, an ecosystem of integrated and reliable software infrastructure is required for spatialtemporal big data management and analysis that will serve as crucial tools for solving a wide set of research problems from different scientific and engineering areas and to empower users with next-generation tools. This vision requires a multidisciplinary effort to significantly advance domain research and have a broad impact on the society. The areas of research discussed in this paper include (i) spatial data mining, (ii) data analytics over remote sensing data, (iii) processing medical images, (iv) spatial econometrics analyses, (v) Map-Reducebased systems for spatial computation and visualization, (vi) CyberGIS systems, and (vii) foundational parallel algorithms and data structures for polygonal datasets, and why HPC infrastructures, including harnessing graphics accelerators, are needed for time-critical applications.

Scalable 3D spatial queries for analytical pathology imaging with MapReduce

3D analytical pathology imaging examines high resolution 3D image volumes of human tissues to facilitate biomedical research and provide potential effective diagnostic assistance. Such approach - quantitative analysis of large- scale 3D pathology image volumes - generates tremendous amounts of spatially derived 3D micro-anatomic objects, such as 3D blood vessels and nuclei. Spatial exploration of such massive 3D spatial data requires effective and efficient querying methods. In this paper, we present a scalable and efficient 3D spatial query system for querying massive 3D spatial data based on MapReduce. The system provides an on-demand spatial querying engine which can be executed with as many instances as needed on MapReduce at runtime. Our system supports multiple types of spatial queries on MapReduce through 3D spatial data partitioning, customizable 3D spatial query engine, and implicit parallel spatial query execution. We utilize multi-level spatial indexing to achieve efficient query processing, including global partition indexing for data retrieval and on-demand local spatial indexing for spatial query processing. We evaluate our system with two representative queries: 3D spatial joins and 3D k-nearest neighbor query. Our experiments demonstrate that our system scales to large number of computing nodes, and efficiently handles data-intensive 3D spatial queries that are challenging in analytical pathology imaging.

Automated level set segmentation of histopathologic cells with sparse shape prior support and dynamic occlusion constraint

In this paper, we propose a novel segmentation method for cells in histopathologic images based on a sparse shape prior guided variational level set framework. We automate the cell contour initialization by detecting seeds and deform contours by minimizing a new energy functional that incorporates a shape term involving sparse shape priors, an adaptive contour occlusion penalty term, and a boundary term encouraging contours to converge to strong edges. As a result, our approach is able to accommodate mutual occlusions and detect contours of multiple intersected cells. We apply our algorithm to a set of whole-slide histopathologic images of brain tumor sections. The proposed method is compared with other popular methods, and demonstrates good accuracy for cell segmentation by quantitative measures, suggesting its promise to support biomedical image-based investigations.

Cloud-Based Whole Slide Image Analysis Using MapReduce

Systematic analysis of high resolution whole slide images enables more effective diagnosis, prognosis and prediction of cancer and other important diseases. Due to the enormous sizes and dimensions of whole slide images, the analysis requires extensive computing resources which are not commonly available. Images have to be divided into smaller regions for processing due to computer memory limitations, which will lead to inaccurate results due to the ignorance of boundary crossing objects. In this paper, we propose a highly scalable and cost effective MapReduce based image analysis framework for whole slide image processing, and provide a cloud based implementation. The framework takes a grid-based overlapping partitioning scheme, and provides parallelization of image segmentation based on MapReduce. It provides graceful handling of boundary objects with a highly efficient spatial indexing based matching method, thus avoiding loss of accuracy due to partitioning. We demonstrate that the system achieves high scalability and is cost-effective --- our experiments demonstrate that it costs less than fifteen cents to analyze one image on average using Amazon Elastic MapReduce.

Robust cell segmentation for histological images of Glioblastoma

Glioblastoma (GBM) is a malignant brain tumor with uniformly dismal prognosis. Quantitative analysis of GBM cells is an important avenue to extract latent histologic disease signatures to correlate with molecular underpinnings and clinical outcomes. As a prerequisite, a robust and accurate cell segmentation is required. In this paper, we present an automated cell segmentation method that can satisfactorily address segmentation of overlapped cells commonly seen in GBM histology specimens. This method first detects cells with seed connectivity, distance constraints, image edge map, and a shape-based voting image. Initialized by identified seeds, cell boundaries are deformed with an improved variational level set method that can handle clumped cells. We test our method on 40 histological images of GBM with human annotations. The validation results suggest that our cell segmentation method is promising and represents an advance in quantitative cancer research.

iSPEED: a scalable and distributed in-memory based spatial query system for large and structurally complex 3D data

The recent technological advancement in digital pathology has enabled 3D tissue-based investigation of human diseases at extremely high resolutions. Discovering and verifying spatial patterns among massive 3D micro-anatomic biological objects such as blood vessels and cells derived from 3D pathology image volumes plays a pivotal role in understanding diseases. However, the exponential increase of available 3D data and the complex structures of biological objects make it extremely difficult to support spatial queries due to high I/O, communication and computational cost for 3D spatial queries. In this demonstration, we present our scalable in-memory based spatial query system iSPEED for large-scale 3D data with complex structures. Low latency is managed by storing in memory with progressive compression including successive levels of detail on object level. On the other hand, low computational cost is achieved by pre-generation of global spatial indexes in memory and additional on-demand generation of indexing at run-time. Furthermore, iSPEED applies structural indexing on complex structured objects in multiple query types to gain performance advantage. During query processing, the memory footprint of iSPEED is minimal due to its indexing structure and progressive decompression on-demand. We demonstrate iSPEED query capability with three representative queries: 3D spatial joins, nearest neighbor and spatial proximity estimation on multiple datasets using a web based RESTful interface. Users can furthermore explore the input data structure, manage and adjust query pipeline parameters on the interface. PVLDB Reference Format: Hoang Vo, Yanhui Liang, Jun Kong, and Fusheng Wang. iSPEED: a Scalable and Distributed In-Memory Based Spatial Query System for Large and Structurally Complex 3D Data.