26,175 research outputs found
Deep Learning for Detection and Segmentation in High-Content Microscopy Images
High-content microscopy led to many advances in biology and medicine. This fast emerging technology is transforming cell biology into a big data driven science. Computer vision methods are used to automate the analysis of microscopy image data. In recent years, deep learning became popular and had major success in computer vision. Most of the available methods are developed to process natural images. Compared to natural images, microscopy images pose domain specific challenges such as small training datasets, clustered objects, and class imbalance.
In this thesis, new deep learning methods for object detection and cell segmentation in microscopy images are introduced. For particle detection in fluorescence microscopy images, a deep learning method based on a domain-adapted Deconvolution Network is presented. In addition, a method for mitotic cell detection in heterogeneous histopathology images is proposed, which combines a deep residual network with Hough voting. The method is used for grading of whole-slide histology images of breast carcinoma. Moreover, a method for both particle detection and cell detection based on object centroids is introduced, which is trainable end-to-end. It comprises a novel Centroid Proposal Network, a layer for ensembling detection hypotheses over image scales and anchors, an anchor regularization scheme which favours prior anchors over regressed locations, and an improved algorithm for Non-Maximum Suppression. Furthermore, a novel loss function based on Normalized Mutual Information is proposed which can cope with strong class imbalance and is derived within a Bayesian framework.
For cell segmentation, a deep neural network with increased receptive field to capture rich semantic information is introduced. Moreover, a deep neural network which combines both paradigms of multi-scale feature aggregation of Convolutional Neural Networks and iterative refinement of Recurrent Neural Networks is proposed. To increase the robustness of the training and improve segmentation, a novel focal loss function is presented.
In addition, a framework for black-box hyperparameter optimization for biomedical image analysis pipelines is proposed. The framework has a modular architecture that separates hyperparameter sampling and hyperparameter optimization. A visualization of the loss function based on infimum projections is suggested to obtain further insights into the optimization problem. Also, a transfer learning approach is presented, which uses only one color channel for pre-training and performs fine-tuning on more color channels. Furthermore, an approach for unsupervised domain adaptation for histopathological slides is presented.
Finally, Galaxy Image Analysis is presented, a platform for web-based microscopy image analysis. Galaxy Image Analysis workflows for cell segmentation in cell cultures, particle detection in mice brain tissue, and MALDI/H&E image registration have been developed.
The proposed methods were applied to challenging synthetic as well as real microscopy image data from various microscopy modalities. It turned out that the proposed methods yield state-of-the-art or improved results. The methods were benchmarked in international image analysis challenges and used in various cooperation projects with biomedical researchers
Blood Cell Classification Using the Hough Transform and Convolutional Neural Networks
https://doi.org/10.1007/978-3-319-77712-2_62The detection of red blood cells in blood samples can be crucial for the disease detection in its early stages. The use of image
processing techniques can accelerate and improve the effectiveness and efficiency of this detection. In this work, the use of the Circle Hough transform for cell detection and artificial neural networks for their identification as a red blood cell is proposed. Specifically, the application of neural networks (MLP) as a standard classification technique with (MLP) is compared with new proposals related to deep learning such as convolutional neural networks (CNNs). The different experiments carried out reveal the high classification ratio and show promising results after the application of the CNNs.Universidad de MĂĄlaga. Campus de Excelencia Internacional AndalucĂa Tech
A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale
In this era of complete genomes, our knowledge of neuroanatomical circuitry
remains surprisingly sparse. Such knowledge is however critical both for basic
and clinical research into brain function. Here we advocate for a concerted
effort to fill this gap, through systematic, experimental mapping of neural
circuits at a mesoscopic scale of resolution suitable for comprehensive,
brain-wide coverage, using injections of tracers or viral vectors. We detail
the scientific and medical rationale and briefly review existing knowledge and
experimental techniques. We define a set of desiderata, including brain-wide
coverage; validated and extensible experimental techniques suitable for
standardization and automation; centralized, open access data repository;
compatibility with existing resources, and tractability with current
informatics technology. We discuss a hypothetical but tractable plan for mouse,
additional efforts for the macaque, and technique development for human. We
estimate that the mouse connectivity project could be completed within five
years with a comparatively modest budget.Comment: 41 page
Augmented Mitotic Cell Count using Field Of Interest Proposal
Histopathological prognostication of neoplasia including most tumor grading
systems are based upon a number of criteria. Probably the most important is the
number of mitotic figures which are most commonly determined as the mitotic
count (MC), i.e. number of mitotic figures within 10 consecutive high power
fields. Often the area with the highest mitotic activity is to be selected for
the MC. However, since mitotic activity is not known in advance, an arbitrary
choice of this region is considered one important cause for high variability in
the prognostication and grading.
In this work, we present an algorithmic approach that first calculates a
mitotic cell map based upon a deep convolutional network. This map is in a
second step used to construct a mitotic activity estimate. Lastly, we select
the image segment representing the size of ten high power fields with the
overall highest mitotic activity as a region proposal for an expert MC
determination. We evaluate the approach using a dataset of 32 completely
annotated whole slide images, where 22 were used for training of the network
and 10 for test. We find a correlation of r=0.936 in mitotic count estimate.Comment: 6 pages, submitted to BVM 2019 (bvm-workshop.org
Class-Agnostic Counting
Nearly all existing counting methods are designed for a specific object
class. Our work, however, aims to create a counting model able to count any
class of object. To achieve this goal, we formulate counting as a matching
problem, enabling us to exploit the image self-similarity property that
naturally exists in object counting problems. We make the following three
contributions: first, a Generic Matching Network (GMN) architecture that can
potentially count any object in a class-agnostic manner; second, by
reformulating the counting problem as one of matching objects, we can take
advantage of the abundance of video data labeled for tracking, which contains
natural repetitions suitable for training a counting model. Such data enables
us to train the GMN. Third, to customize the GMN to different user
requirements, an adapter module is used to specialize the model with minimal
effort, i.e. using a few labeled examples, and adapting only a small fraction
of the trained parameters. This is a form of few-shot learning, which is
practical for domains where labels are limited due to requiring expert
knowledge (e.g. microbiology). We demonstrate the flexibility of our method on
a diverse set of existing counting benchmarks: specifically cells, cars, and
human crowds. The model achieves competitive performance on cell and crowd
counting datasets, and surpasses the state-of-the-art on the car dataset using
only three training images. When training on the entire dataset, the proposed
method outperforms all previous methods by a large margin.Comment: Asian Conference on Computer Vision (ACCV), 201
Stacked Denoising Autoencoders and Transfer Learning for Immunogold Particles Detection and Recognition
In this paper we present a system for the detection of immunogold particles
and a Transfer Learning (TL) framework for the recognition of these immunogold
particles. Immunogold particles are part of a high-magnification method for the
selective localization of biological molecules at the subcellular level only
visible through Electron Microscopy. The number of immunogold particles in the
cell walls allows the assessment of the differences in their compositions
providing a tool to analise the quality of different plants. For its
quantization one requires a laborious manual labeling (or annotation) of images
containing hundreds of particles. The system that is proposed in this paper can
leverage significantly the burden of this manual task.
For particle detection we use a LoG filter coupled with a SDA. In order to
improve the recognition, we also study the applicability of TL settings for
immunogold recognition. TL reuses the learning model of a source problem on
other datasets (target problems) containing particles of different sizes. The
proposed system was developed to solve a particular problem on maize cells,
namely to determine the composition of cell wall ingrowths in endosperm
transfer cells. This novel dataset as well as the code for reproducing our
experiments is made publicly available.
We determined that the LoG detector alone attained more than 84\% of accuracy
with the F-measure. Developing immunogold recognition with TL also provided
superior performance when compared with the baseline models augmenting the
accuracy rates by 10\%
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