VGG-UNet/VGG-SegNet Supported Automatic Segmentation of Endoplasmic Reticulum Network in Fluorescence Microscopy Images.

This research work aims to implement an automated segmentation process to extract the endoplasmic reticulum (ER) network in fluorescence microscopy images (FMI) using pretrained convolutional neural network (CNN). The threshold level of the raw FMT is complex, and extraction of the ER network is a challenging task. Hence, an image conversion procedure is initially employed to reduce its complexity. This work employed the pretrained CNN schemes, such as VGG-UNet and VGG-SegNet, to mine the ER network from the chosen FMI test images. The proposed ER segmentation pipeline consists of the following phases; (i) clinical image collection, 16-bit to 8-bit conversion and resizing; (ii) implementation of pretrained VGG-UNet and VGG-SegNet; (iii) extraction of the binary form of ER network; (iv) comparing the mined ER with ground-truth; and (v) computation of image measures and validation. The considered FMI dataset consists of 223 test images, and image augmentation is then implemented to increase these images. The result of this scheme is then confirmed against other CNN methods, such as U-Net, SegNet, and Res-UNet. The experimental outcome confirms a segmentation accuracy of >98% with VGG-UNet and VGG-SegNet. The results of this research authenticate that the proposed pipeline can be considered to examine the clinical-grade FMI.

Deep learning supported disease detection with multi-modality image fusion.

Multi-modal image fusion techniques aid the medical experts in better disease diagnosis by providing adequate complementary information from multi-modal medical images. These techniques enhance the effectiveness of medical disorder analysis and classification of results. This study aims at proposing a novel technique using deep learning for the fusion of multi-modal medical images. The modified 2D Adaptive Bilateral Filters (M-2D-ABF) algorithm is used in the image pre-processing for filtering various types of noises. The contrast and brightness are improved by applying the proposed Energy-based CLAHE algorithm in order to preserve the high energy regions of the multimodal images. Images from two different modalities are first registered using mutual information and then registered images are fused to form a single image. In the proposed fusion scheme, images are fused using Siamese Neural Network and Entropy (SNNE)-based image fusion algorithm. Particularly, the medical images are fused by using Siamese convolutional neural network structure and the entropy of the images. Fusion is done on the basis of score of the SoftMax layer and the entropy of the image. The fused image is segmented using Fast Fuzzy C Means Clustering Algorithm (FFCMC) and Otsu Thresholding. Finally, various features are extracted from the segmented regions. Using the extracted features, classification is done using Logistic Regression classifier. Evaluation is performed using publicly available benchmark dataset. Experimental results using various pairs of multi-modal medical images reveal that the proposed multi-modal image fusion and classification techniques compete the existing state-of-the-art techniques reported in the literature.

Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer.

Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial-to-mesenchymal transition and cancer stem cell activities. The architectural organization of regulatory machinery is addressed within the contexts of translating cancer-compromised genomic organization to advances in breast cancer risk assessment, diagnosis, prognosis, and identification of novel therapeutic targets with high specificity and minimal off target effects.

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types.

BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource.