1,080 research outputs found
Developing the Quantitative Histopathology Image Ontology : A case study using the hot spot detection problem
Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts
GAN-based Virtual Re-Staining: A Promising Solution for Whole Slide Image Analysis
Histopathological cancer diagnosis is based on visual examination of stained
tissue slides. Hematoxylin and eosin (H\&E) is a standard stain routinely
employed worldwide. It is easy to acquire and cost effective, but cells and
tissue components show low-contrast with varying tones of dark blue and pink,
which makes difficult visual assessments, digital image analysis, and
quantifications. These limitations can be overcome by IHC staining of target
proteins of the tissue slide. IHC provides a selective, high-contrast imaging
of cells and tissue components, but their use is largely limited by a
significantly more complex laboratory processing and high cost. We proposed a
conditional CycleGAN (cCGAN) network to transform the H\&E stained images into
IHC stained images, facilitating virtual IHC staining on the same slide. This
data-driven method requires only a limited amount of labelled data but will
generate pixel level segmentation results. The proposed cCGAN model improves
the original network \cite{zhu_unpaired_2017} by adding category conditions and
introducing two structural loss functions, which realize a multi-subdomain
translation and improve the translation accuracy as well. % need to give
reasons here. Experiments demonstrate that the proposed model outperforms the
original method in unpaired image translation with multi-subdomains. We also
explore the potential of unpaired images to image translation method applied on
other histology images related tasks with different staining techniques
Machine learning methods for histopathological image analysis
Abundant accumulation of digital histopathological images has led to the
increased demand for their analysis, such as computer-aided diagnosis using
machine learning techniques. However, digital pathological images and related
tasks have some issues to be considered. In this mini-review, we introduce the
application of digital pathological image analysis using machine learning
algorithms, address some problems specific to such analysis, and propose
possible solutions.Comment: 23 pages, 4 figure
The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain
The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals
SHIRAZ: an automated histology image annotation system for zebrafish phenomics
Histological characterization is used in clinical and research contexts as a highly sensitive method for detecting the morphological features of disease and abnormal gene function. Histology has recently been accepted as a phenotyping method for the forthcoming Zebrafish Phenome Project, a large-scale community effort to characterize the morphological, physiological, and behavioral phenotypes resulting from the mutations in all known genes in the zebrafish genome. In support of this project, we present a novel content-based image retrieval system for the automated annotation of images containing histological abnormalities in the developing eye of the larval zebrafish
Deep active learning for suggestive segmentation of biomedical image stacks via optimisation of Dice scores and traced boundary length
Manual segmentation of stacks of 2D biomedical images (e.g., histology) is a time-consuming task which can be sped up with semi-automated techniques. In this article, we present a suggestive deep active learning framework that seeks to minimise the annotation effort required to achieve a certain level of accuracy when labelling such a stack. The framework suggests, at every iteration, a specific region of interest (ROI) in one of the images for manual delineation. Using a deep segmentation neural network and a mixed cross-entropy loss function, we propose a principled strategy to estimate class probabilities for the whole stack, conditioned on heterogeneous partial segmentations of the 2D images, as well as on weak supervision in the form of image indices that bound each ROI. Using the estimated probabilities, we propose a novel active learning criterion based on predictions for the estimated segmentation performance and delineation effort, measured with average Dice scores and total delineated boundary length, respectively, rather than common surrogates such as entropy. The query strategy suggests the ROI that is expected to maximise the ratio between performance and effort, while considering the adjacency of structures that may have already been labelled – which decrease the length of the boundary to trace. We provide quantitative results on synthetically deformed MRI scans and real histological data, showing that our framework can reduce labelling effort by up to 60–70% without compromising accuracy
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