Semi-automatic watershed merging method

Watershed transformation frequently produces over-segmented images. The authorspropose a solution to this problem. It utilizes hierarchical cluster analysis for grouping watershedswhich are treated as objects characterized by a number of attributes. Initially the watershed mergingmethod was meant only for gray-scale images, but later it was adapted for colour images. This paperpresents further extension of the method that allows it to either automatically select the numberof classes or to provide a hint as to which numbers in a specified range should be considered first.Segmentation quality assessment functions for colour images are presented. The results obtained usingan extended watershed merging method are discussed. The examples of segmentations selected by themethod, along with the graphs of assessment functions, are shown

Cell Segmentation in 3D Confocal Images using Supervoxel Merge-Forests with CNN-based Hypothesis Selection

Automated segmentation approaches are crucial to quantitatively analyze large-scale 3D microscopy images. Particularly in deep tissue regions, automatic methods still fail to provide error-free segmentations. To improve the segmentation quality throughout imaged samples, we present a new supervoxel-based 3D segmentation approach that outperforms current methods and reduces the manual correction effort. The algorithm consists of gentle preprocessing and a conservative super-voxel generation method followed by supervoxel agglomeration based on local signal properties and a postprocessing step to fix under-segmentation errors using a Convolutional Neural Network. We validate the functionality of the algorithm on manually labeled 3D confocal images of the plant Arabidopis thaliana and compare the results to a state-of-the-art meristem segmentation algorithm.Comment: 5 pages, 3 figures, 1 tabl

Machine learning of hierarchical clustering to segment 2D and 3D images

We aim to improve segmentation through the use of machine learning tools during region agglomeration. We propose an active learning approach for performing hierarchical agglomerative segmentation from superpixels. Our method combines multiple features at all scales of the agglomerative process, works for data with an arbitrary number of dimensions, and scales to very large datasets. We advocate the use of variation of information to measure segmentation accuracy, particularly in 3D electron microscopy (EM) images of neural tissue, and using this metric demonstrate an improvement over competing algorithms in EM and natural images.Comment: 15 pages, 8 figure

Guided Proofreading of Automatic Segmentations for Connectomics

Automatic cell image segmentation methods in connectomics produce merge and split errors, which require correction through proofreading. Previous research has identified the visual search for these errors as the bottleneck in interactive proofreading. To aid error correction, we develop two classifiers that automatically recommend candidate merges and splits to the user. These classifiers use a convolutional neural network (CNN) that has been trained with errors in automatic segmentations against expert-labeled ground truth. Our classifiers detect potentially-erroneous regions by considering a large context region around a segmentation boundary. Corrections can then be performed by a user with yes/no decisions, which reduces variation of information 7.5x faster than previous proofreading methods. We also present a fully-automatic mode that uses a probability threshold to make merge/split decisions. Extensive experiments using the automatic approach and comparing performance of novice and expert users demonstrate that our method performs favorably against state-of-the-art proofreading methods on different connectomics datasets.Comment: Supplemental material available at http://rhoana.org/guidedproofreading/supplemental.pd

From lumped to distributed via semi-distributed: Calibration strategies for semi-distributed hydrologic models

Modeling the effect of spatial variability of precipitation and basin characteristics on streamflow requires the use of distributed or semi-distributed hydrologic models. This paper addresses a DMIP 2 study that focuses on the advantages of using a semi-distributed modeling structure. We first present a revised semi-distributed structure of the NWS SACramento Soil Moisture Accounting (SAC-SMA) model that separates the routing of fast and slow response runoff components, and thus explicitly accounts for the differences between the two components. We then test four different calibration strategies that take advantage of the strengths of existing optimization algorithms (SCE-UA) and schemes (MACS). These strategies include: (1) lumped parameters and basin averaged precipitation, (2) semi-lumped parameters and distributed precipitation forcing, (3) semi-distributed parameters and distributed precipitation forcing and (4) lumped parameters and basin averaged precipitation, modified using a priori parameters of the SAC-SMA model. Finally, we explore the value of using discharge observations at interior points in model calibration by assessing gains/losses in hydrograph simulations at the basin outlet. Our investigation focuses on two key DMIP 2 science questions. Specifically, we investigate (a) the ability of the semi-distributed model structure to improve stream flow simulations at the basin outlet and (b) to provide reasonably good simulations at interior points.The semi-distributed model is calibrated for the Illinois River Basin at Siloam Springs, Arkansas using streamflow observations at the basin outlet only. The results indicate that lumped to distributed calibration strategies (1 and 4) both improve simulation at the outlet and provide meaningful streamflow predictions at interior points. In addition, the results of the complementary study, which uses interior points during the model calibration, suggest that model performance at the outlet can be further improved by using a semi-distributed structure calibrated at both interior points and the outlet, even when only a few years of historical record are available. © 2009 Elsevier B.V

A video object generation tool allowing friendly user interaction

In this paper we describe an interactive video object segmentation tool developed in the framework of the ACTS-AC098 MOMUSYS project. The Video Object Generator with User Environment (VOGUE) combines three different sets of automatic and semi-automatic-tool (spatial segmentation, object tracking and temporal segmentation) with general purpose tools for user interaction. The result is an integrated environment allowing the user-assisted segmentation of any sort of video sequences in a friendly and efficient manner.Peer ReviewedPostprint (published version

Segmentation of ultrasound images of thyroid nodule for assisting fine needle aspiration cytology

The incidence of thyroid nodule is very high and generally increases with the age. Thyroid nodule may presage the emergence of thyroid cancer. The thyroid nodule can be completely cured if detected early. Fine needle aspiration cytology is a recognized early diagnosis method of thyroid nodule. There are still some limitations in the fine needle aspiration cytology, and the ultrasound diagnosis of thyroid nodule has become the first choice for auxiliary examination of thyroid nodular disease. If we could combine medical imaging technology and fine needle aspiration cytology, the diagnostic rate of thyroid nodule would be improved significantly. The properties of ultrasound will degrade the image quality, which makes it difficult to recognize the edges for physicians. Image segmentation technique based on graph theory has become a research hotspot at present. Normalized cut (Ncut) is a representative one, which is suitable for segmentation of feature parts of medical image. However, how to solve the normalized cut has become a problem, which needs large memory capacity and heavy calculation of weight matrix. It always generates over segmentation or less segmentation which leads to inaccurate in the segmentation. The speckle noise in B ultrasound image of thyroid tumor makes the quality of the image deteriorate. In the light of this characteristic, we combine the anisotropic diffusion model with the normalized cut in this paper. After the enhancement of anisotropic diffusion model, it removes the noise in the B ultrasound image while preserves the important edges and local details. This reduces the amount of computation in constructing the weight matrix of the improved normalized cut and improves the accuracy of the final segmentation results. The feasibility of the method is proved by the experimental results.Comment: 15pages,13figure