SFCN-OPI: Detection and Fine-grained Classification of Nuclei Using Sibling FCN with Objectness Prior Interaction

Cell nuclei detection and fine-grained classification have been fundamental yet challenging problems in histopathology image analysis. Due to the nuclei tiny size, significant inter-/intra-class variances, as well as the inferior image quality, previous automated methods would easily suffer from limited accuracy and robustness. In the meanwhile, existing approaches usually deal with these two tasks independently, which would neglect the close relatedness of them. In this paper, we present a novel method of sibling fully convolutional network with prior objectness interaction (called SFCN-OPI) to tackle the two tasks simultaneously and interactively using a unified end-to-end framework. Specifically, the sibling FCN branches share features in earlier layers while holding respective higher layers for specific tasks. More importantly, the detection branch outputs the objectness prior which dynamically interacts with the fine-grained classification sibling branch during the training and testing processes. With this mechanism, the fine-grained classification successfully focuses on regions with high confidence of nuclei existence and outputs the conditional probability, which in turn benefits the detection through back propagation. Extensive experiments on colon cancer histology images have validated the effectiveness of our proposed SFCN-OPI and our method has outperformed the state-of-the-art methods by a large margin.Comment: Accepted at AAAI 201

Метод сегментации перекрывающихся форменных элементов крови на микроскопических медицинских изображениях

Рассматривается решение задачи эритроцитометрии с использованием методов компьютерного зрени

Automatic Leukemia Cell Counting using Iterative Distance Transform for Convex Sets

The calculation of white blood cells on the acute leukemia microscopic images is one of the stages in the diagnosis of Leukemia disease. The main constraint on calculating the number of white blood cells is the precision in the area of overlapping white blood cells. The research on the calculation of the number of white blood cells overlapping generally based on geometry. However, there was still a calculation error due to over segment or under segment. This paper proposed an Iterative Distance Transform for Convex Sets (IDTCS) method to determine the markers and calculate the number of overlapping white blood cells. Determination of marker was performed on every cell both in single and overlapping white blood cell area. In this study, there were tree stages: segmentation of white blood cells, marker detection and white blood cell count, and contour estimation of every white blood cell. The used data testing was microscopic acute leukemia image data of Acute Lymphoblastic Leukemia (ALL) and Acute Myeloblastic Leukemia (AML). Based on the test results, Iterative Distance Transform for Convex Sets IDTCS method performs better than Distance Transform (DT) and Ultimate Erosion for Convex Sets (UECS) method

Segmentation of Carpal Bones Using Gradient Inverse Coefficient of Variation with Dynamic Programming Method

Segmentation of the carpal bones (CBs) especially for children above seven years old is a challenging task in computer vision mainly because of poor definitions of the bone contours and the occurrence of the partial overlapping of the bones. Although active contour methods are widely employed in image bone segmentation, they are sensitive to initialization and have limitation in segmenting overlapping objects.  Thus, there is a need for a robust segmentation method for bone segmentation. This paper presents an automatic active boundary-based segmentation method, gradient inverse coefficient of variation, based on dynamic programming (DP-GICOV) method to segment carpal bones on radiographic images of children age 5 to 8 years old. A mapping procedure is designed based on a priori knowledge about the natural growth and the arrangement of carpal bones in human body. The accuracy of the DP-GICOV is compared qualitatively and quantitatively with the de-regularized level set (DRLS) and multi-scale gradient vector flow (MGVF) on a dataset of 20 images of carpal bones from University of Southern California. The presented method is capable to detect the bone boundaries fast and accurate. Results show that the DP-GICOV is highly accurate especially for overlapping bones, which is more than 85% in many cases, and it requires minimal user’s intervention. This method has produced a promised result in overcoming both issues faced by active contours method; initialization and overlapping objects

Statistically Representative Metrology of Nanoparticles via Unsupervised Machine Learning of TEM Images

The morphology of nanoparticles governs their properties for a range of important applica tions. Thus, the ability to statistically correlate this key particle performance parameter is paramount in achieving accurate control of nanoparticle properties. Among several effective techniques for morphological characterization of nanoparticles, transmission electron microscopy (TEM) can pro vide a direct, accurate characterization of the details of nanoparticle structures and morphology at atomic resolution. However, manually analyzing a large number of TEM images is laborious. In this work, we demonstrate an efficient, robust and highly automated unsupervised machine learning method for the metrology of nanoparticle systems based on TEM images. Our method not only can achieve statistically significant analysis, but it is also robust against variable image quality, imaging modalities, and particle dispersions. The ability to efficiently gain statistically significant particle metrology is critical in advancing precise particle synthesis and accurate property control.Australia Research Council (ARC) IC210100056Ministerio de Economía y Competitividad TIN2014-55894-C2-RMinisterio de Economía y Competitividad TIN2017-88209-C2-2-

The role of electron irradiation history in liquid cell transmission electron microscopy.

In situ liquid cell transmission electron microscopy (LC-TEM) allows dynamic nanoscale characterization of systems in a hydrated state. Although powerful, this technique remains impaired by issues of repeatability that limit experimental fidelity and hinder the identification and control of some variables underlying observed dynamics. We detail new LC-TEM devices that improve experimental reproducibility by expanding available imaging area and providing a platform for investigating electron flux history on the sample. Irradiation history is an important factor influencing LC-TEM results that has, to this point, been largely qualitatively and not quantitatively described. We use these devices to highlight the role of cumulative electron flux history on samples from both nanoparticle growth and biological imaging experiments and demonstrate capture of time zero, low-dose images on beam-sensitive samples. In particular, the ability to capture pristine images of biological samples, where the acquired image is the first time that the cell experiences significant electron flux, allowed us to determine that nanoparticle movement compared to the cell membrane was a function of cell damage and therefore an artifact rather than visualizing cell dynamics in action. These results highlight just a subset of the new science that is accessible with LC-TEM through the new multiwindow devices with patterned focusing aides