Deep Learning Image Classification of Red Blood Cell Deformability

Red blood cells (RBCs) must be highly deformable to transit through the microvasculature to deliver oxygen to tissues. The loss of RBC deformability resulting from pathology, natural aging, or storage in blood bags can impede the proper function of these cells. A variety of methods have been developed to measure RBC deformability, but these methods require specialized equipment, long measurement time, and highly skilled personnel. To address this challenge, we investigated whether a machine learning approach could be applied to determine donor RBC deformability using single cell microscope images. We used the microfluidic ratchet device to sort RBCs based on deformability. Sorted cells are then imaged and used to train a deep learning model to classify RBCs based on deformability. This model correctly predicted deformability of individual RBCs with 84 ± 11% accuracy averaged across ten donors. Using this model to score the deformability of RBC samples were accurate to within 4.4 ± 2.5% of the value obtained using the microfluidic ratchet device. While machine learning methods are frequently developed to automate human image analysis, our study is remarkable in showing that deep learning of single cell microscopy images could be used to measure RBC deformability, a property not normally measurable by imaging. Measuring RBC deformability by imaging is also desirable because it can be performed rapidly using a standard microscopy system, potentially enabling RBC deformability studies to be performed as part of routine clinical assessments.

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Assessing Red Blood Cell Deformability using Deep Learning

Lab on a Chip ◽

10.1039/d1lc01006a ◽

2021 ◽

Author(s):

Erik S. Lamoureux ◽

Emel Islamzada ◽

Matthew V.J. Wiens ◽

Kerryn Matthews ◽

Simon P. Duffy ◽

...

Keyword(s):

Deep Learning ◽

Blood Cell ◽

Red Blood Cells ◽

Red Blood Cell ◽

Blood Cells ◽

Natural Aging ◽

Cell Deformability ◽

Red Blood Cell Deformability ◽

Rbc Deformability

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Single-Cell Phenotype Classification Using Deep Convolutional Neural Networks

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057116631284 ◽

2016 ◽

Vol 21 (9) ◽

pp. 998-1003 ◽

Cited By ~ 42

Author(s):

Oliver Dürr ◽

Beate Sick

Keyword(s):

Machine Learning ◽

Neural Networks ◽

Deep Learning ◽

Single Cell ◽

Convolutional Neural Networks ◽

State Of The Art ◽

Misclassification Rate ◽

Support Vector ◽

Learning Methods ◽

Phenotype Classification

Deep learning methods are currently outperforming traditional state-of-the-art computer vision algorithms in diverse applications and recently even surpassed human performance in object recognition. Here we demonstrate the potential of deep learning methods to high-content screening–based phenotype classification. We trained a deep learning classifier in the form of convolutional neural networks with approximately 40,000 publicly available single-cell images from samples treated with compounds from four classes known to lead to different phenotypes. The input data consisted of multichannel images. The construction of appropriate feature definitions was part of the training and carried out by the convolutional network, without the need for expert knowledge or handcrafted features. We compare our results against the recent state-of-the-art pipeline in which predefined features are extracted from each cell using specialized software and then fed into various machine learning algorithms (support vector machine, Fisher linear discriminant, random forest) for classification. The performance of all classification approaches is evaluated on an untouched test image set with known phenotype classes. Compared to the best reference machine learning algorithm, the misclassification rate is reduced from 8.9% to 6.6%.

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DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning

10.1101/720615 ◽

2019 ◽

Cited By ~ 5

Author(s):

Jean-Baptiste Lugagne ◽

Haonan Lin ◽

Mary J. Dunlop

Keyword(s):

Gene Expression ◽

Machine Learning ◽

Image Analysis ◽

Deep Learning ◽

Single Cell ◽

Real Time ◽

Microfluidic Device ◽

Time Lapse ◽

Cell Segmentation ◽

Analysis Pipeline

AbstractMicroscopy image analysis is a major bottleneck in quantification of single-cell microscopy data, typically requiring human supervision and curation, which limit both accuracy and throughput. To address this, we developed a deep learning-based image analysis pipeline that performs segmentation, tracking, and lineage reconstruction. Our analysis focuses on time-lapse movies of Escherichia coli cells trapped in a “mother machine” microfluidic device, a scalable platform for long-term single-cell analysis that is widely used in the field. While deep learning has been applied to cell segmentation problems before, our approach is fundamentally innovative in that it also uses machine learning to perform cell tracking and lineage reconstruction. With this framework we are able to get high fidelity results (1% error rate), without human supervision. Further, the algorithm is fast, with complete analysis of a typical frame containing ∼150 cells taking <700msec. The framework is not constrained to a particular experimental set up and has the potential to generalize to time-lapse images of other organisms or different experimental configurations. These advances open the door to a myriad of applications including real-time tracking of gene expression and high throughput analysis of strain libraries at single-cell resolution.Author SummaryAutomated microscopy experiments can generate massive data sets, allowing for detailed analysis of cell physiology and properties such as gene expression. In particular, dynamic measurements of gene expression with time-lapse microscopy have proved invaluable for understanding how gene regulatory networks operate. However, image analysis remains a key bottleneck in the analysis pipeline, typically requiring human supervision and a posteriori processing. Recently, machine learning-based approaches have ushered in a new era of rapid, unsupervised image analysis. In this work, we use and repurpose the U-Net deep learning algorithm to develop an image processing pipeline that can not only accurately identify the location of cells in an image, but also track them over time as they grow and divide. As an application, we focus on multi-hour time-lapse movies of bacteria growing in a microfluidic device. Our algorithm is accurate and fast, with error rates near 1% and requiring less than a second to analyze a typical movie frame. This increase in speed and fidelity has the potential to open new experimental avenues, e.g. where images are analyzed on-the-fly so that experimental conditions can be updated in real time.

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Deep learning does not outperform classical machine learning for cell-type annotation

10.1101/653907 ◽

2019 ◽

Cited By ~ 7

Author(s):

Niklas D. Köhler ◽

Maren Büttner ◽

Fabian J. Theis

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Single Cell ◽

Language Processing ◽

Word Identification ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cell Types ◽

Learning Approaches ◽

Cell Type

AbstractDeep learning has revolutionized image analysis and natural language processing with remarkable accuracies in prediction tasks, such as image labeling or word identification. The origin of this revolution was arguably the deep learning approach by the Hinton lab in 2012, which halved the error rate of existing classifiers in the then 2-year-old ImageNet database1. In hindsight, the combination of algorithmic and hardware advances with the appearance of large and well-labeled datasets has led up to this seminal contribution.The emergence of large amounts of data from single-cell RNA-seq and the recent global effort to chart all cell types in the Human Cell Atlas has attracted an interest in deep-learning applications. However, all current approaches are unsupervised, i.e., learning of latent spaces without using any cell labels, even though supervised learning approaches are often more powerful in feature learning and the most popular approach in the current AI revolution by far.Here, we ask why this is the case. In particular we ask whether supervised deep learning can be used for cell annotation, i.e. to predict cell-type labels from single-cell gene expression profiles. After evaluating 6 classification methods across 14 datasets, we notably find that deep learning does not outperform classical machine-learning methods in the task. Thus, cell-type prediction based on gene-signature derived cell-type labels is potentially too simplistic a task for complex non-linear methods, which demands better labels of functional single-cell readouts. We, therefore, are still waiting for the “ImageNet moment” in single-cell genomics.

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Deep Learning Based High-Resolution Remote Sensing Image classification

International Journal of Advanced Research in Computer Science and Software Engineering ◽

10.23956/ijarcsse.v7i10.384 ◽

2017 ◽

Vol 7 (10) ◽

pp. 22

Author(s):

Sumit Kaur

Keyword(s):

Machine Learning ◽

Remote Sensing ◽

Deep Learning ◽

Image Classification ◽

Language Processing ◽

Object Perception ◽

Remote Sensing Image ◽

Research Area ◽

Remote Sensing Image Classification ◽

Unsupervised Algorithms

Abstract- Deep learning is an emerging research area in machine learning and pattern recognition field which has been presented with the goal of drawing Machine Learning nearer to one of its unique objectives, Artificial Intelligence. It tries to mimic the human brain, which is capable of processing and learning from the complex input data and solving different kinds of complicated tasks well. Deep learning (DL) basically based on a set of supervised and unsupervised algorithms that attempt to model higher level abstractions in data and make it self-learning for hierarchical representation for classification. In the recent years, it has attracted much attention due to its state-of-the-art performance in diverse areas like object perception, speech recognition, computer vision, collaborative filtering and natural language processing. This paper will present a survey on different deep learning techniques for remote sensing image classification.

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Data science in economics: comprehensive review of advanced machine learning and deep learning methods

10.31232/osf.io/4pxq2 ◽

2020 ◽

Author(s):

Saeed Nosratabadi ◽

Amir Mosavi ◽

Puhong Duan ◽

Pedram Ghamisi ◽

Ferdinand Filip ◽

...

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Data Science ◽

State Of The Art ◽

Science Methods ◽

Learning Models ◽

Diverse Range ◽

Hybrid Machine ◽

Economics Research

This paper provides a state-of-the-art investigation of advances in data science in emerging economic applications. The analysis was performed on novel data science methods in four individual classes of deep learning models, hybrid deep learning models, hybrid machine learning, and ensemble models. Application domains include a wide and diverse range of economics research from the stock market, marketing, and e-commerce to corporate banking and cryptocurrency. Prisma method, a systematic literature review methodology, was used to ensure the quality of the survey. The findings reveal that the trends follow the advancement of hybrid models, which, based on the accuracy metric, outperform other learning algorithms. It is further expected that the trends will converge toward the advancements of sophisticated hybrid deep learning models.

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Deep Learning for text in limted data settings

10.36227/techrxiv.12100692 ◽

2020 ◽

Author(s):

Pathikkumar Patel ◽

Bhargav Lad ◽

Jinan Fiaidhi

Keyword(s):

Machine Learning ◽

Time Series ◽

Deep Learning ◽

Sentiment Analysis ◽

Transfer Learning ◽

Text Classification ◽

State Of The Art ◽

Time Series Forecasting ◽

Text Data ◽

Performance Levels

During the last few years, RNN models have been extensively used and they have proven to be better for sequence and text data. RNNs have achieved state-of-the-art performance levels in several applications such as text classification, sequence to sequence modelling and time series forecasting. In this article we will review different Machine Learning and Deep Learning based approaches for text data and look at the results obtained from these methods. This work also explores the use of transfer learning in NLP and how it affects the performance of models on a specific application of sentiment analysis.

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