Automated multi-class ground-truth labeling of H&E images for deep learning using multiplexed fluorescence microscopy

Author(s):  
Gouthamrajan Nadarajan ◽  
Tyna Hope ◽  
Dan Wang ◽  
Allison Cheung ◽  
Fiona Ginty ◽  
...  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Crouzet ◽  
Gwangjin Jeong ◽  
Rachel H. Chae ◽  
Krystal T. LoPresti ◽  
Cody E. Dunn ◽  
...  

AbstractCerebral microhemorrhages (CMHs) are associated with cerebrovascular disease, cognitive impairment, and normal aging. One method to study CMHs is to analyze histological sections (5–40 μm) stained with Prussian blue. Currently, users manually and subjectively identify and quantify Prussian blue-stained regions of interest, which is prone to inter-individual variability and can lead to significant delays in data analysis. To improve this labor-intensive process, we developed and compared three digital pathology approaches to identify and quantify CMHs from Prussian blue-stained brain sections: (1) ratiometric analysis of RGB pixel values, (2) phasor analysis of RGB images, and (3) deep learning using a mask region-based convolutional neural network. We applied these approaches to a preclinical mouse model of inflammation-induced CMHs. One-hundred CMHs were imaged using a 20 × objective and RGB color camera. To determine the ground truth, four users independently annotated Prussian blue-labeled CMHs. The deep learning and ratiometric approaches performed better than the phasor analysis approach compared to the ground truth. The deep learning approach had the most precision of the three methods. The ratiometric approach has the most versatility and maintained accuracy, albeit with less precision. Our data suggest that implementing these methods to analyze CMH images can drastically increase the processing speed while maintaining precision and accuracy.


2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii359-iii359
Author(s):  
Lydia Tam ◽  
Edward Lee ◽  
Michelle Han ◽  
Jason Wright ◽  
Leo Chen ◽  
...  

Abstract BACKGROUND Brain tumors are the most common solid malignancies in childhood, many of which develop in the posterior fossa (PF). Manual tumor measurements are frequently required to optimize registration into surgical navigation systems or for surveillance of nonresectable tumors after therapy. With recent advances in artificial intelligence (AI), automated MRI-based tumor segmentation is now feasible without requiring manual measurements. Our goal was to create a deep learning model for automated PF tumor segmentation that can register into navigation systems and provide volume output. METHODS 720 pre-surgical MRI scans from five pediatric centers were divided into training, validation, and testing datasets. The study cohort comprised of four PF tumor types: medulloblastoma, diffuse midline glioma, ependymoma, and brainstem or cerebellar pilocytic astrocytoma. Manual segmentation of the tumors by an attending neuroradiologist served as “ground truth” labels for model training and evaluation. We used 2D Unet, an encoder-decoder convolutional neural network architecture, with a pre-trained ResNet50 encoder. We assessed ventricle segmentation accuracy on a held-out test set using Dice similarity coefficient (0–1) and compared ventricular volume calculation between manual and model-derived segmentations using linear regression. RESULTS Compared to the ground truth expert human segmentation, overall Dice score for model performance accuracy was 0.83 for automatic delineation of the 4 tumor types. CONCLUSIONS In this multi-institutional study, we present a deep learning algorithm that automatically delineates PF tumors and outputs volumetric information. Our results demonstrate applied AI that is clinically applicable, potentially augmenting radiologists, neuro-oncologists, and neurosurgeons for tumor evaluation, surveillance, and surgical planning.


Author(s):  
Alvaro Gomariz ◽  
Tiziano Portenier ◽  
Patrick M. Helbling ◽  
Stephan Isringhausen ◽  
Ute Suessbier ◽  
...  

2021 ◽  
pp. 1-14
Author(s):  
Waqas Yousaf ◽  
Arif Umar ◽  
Syed Hamad Shirazi ◽  
Zakir Khan ◽  
Imran Razzak ◽  
...  

Automatic logo detection and recognition is significantly growing due to the increasing requirements of intelligent documents analysis and retrieval. The main problem to logo detection is intra-class variation, which is generated by the variation in image quality and degradation. The problem of misclassification also occurs while having tiny logo in large image with other objects. To address this problem, Patch-CNN is proposed for logo recognition which uses small patches of logos for training to solve the problem of misclassification. The classification is accomplished by dividing the logo images into small patches and threshold is applied to drop no logo area according to ground truth. The architectures of AlexNet and ResNet are also used for logo detection. We propose a segmentation free architecture for the logo detection and recognition. In literature, the concept of region proposal generation is used to solve logo detection, but these techniques suffer in case of tiny logos. Proposed CNN is especially designed for extracting the detailed features from logo patches. So far, the technique has attained accuracy equals to 0.9901 with acceptable training and testing loss on the dataset used in this work.


Algorithms ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 212
Author(s):  
Youssef Skandarani ◽  
Pierre-Marc Jodoin ◽  
Alain Lalande

Deep learning methods are the de facto solutions to a multitude of medical image analysis tasks. Cardiac MRI segmentation is one such application, which, like many others, requires a large number of annotated data so that a trained network can generalize well. Unfortunately, the process of having a large number of manually curated images by medical experts is both slow and utterly expensive. In this paper, we set out to explore whether expert knowledge is a strict requirement for the creation of annotated data sets on which machine learning can successfully be trained. To do so, we gauged the performance of three segmentation models, namely U-Net, Attention U-Net, and ENet, trained with different loss functions on expert and non-expert ground truth for cardiac cine–MRI segmentation. Evaluation was done with classic segmentation metrics (Dice index and Hausdorff distance) as well as clinical measurements, such as the ventricular ejection fractions and the myocardial mass. The results reveal that generalization performances of a segmentation neural network trained on non-expert ground truth data is, to all practical purposes, as good as that trained on expert ground truth data, particularly when the non-expert receives a decent level of training, highlighting an opportunity for the efficient and cost-effective creation of annotations for cardiac data sets.


Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4582
Author(s):  
Changjie Cai ◽  
Tomoki Nishimura ◽  
Jooyeon Hwang ◽  
Xiao-Ming Hu ◽  
Akio Kuroda

Fluorescent probes can be used to detect various types of asbestos (serpentine and amphibole groups); however, the fiber counting using our previously developed software was not accurate for samples with low fiber concentration. Machine learning-based techniques (e.g., deep learning) for image analysis, particularly Convolutional Neural Networks (CNN), have been widely applied to many areas. The objectives of this study were to (1) create a database of a wide-range asbestos concentration (0–50 fibers/liter) fluorescence microscopy (FM) images in the laboratory; and (2) determine the applicability of the state-of-the-art object detection CNN model, YOLOv4, to accurately detect asbestos. We captured the fluorescence microscopy images containing asbestos and labeled the individual asbestos in the images. We trained the YOLOv4 model with the labeled images using one GTX 1660 Ti Graphics Processing Unit (GPU). Our results demonstrated the exceptional capacity of the YOLOv4 model to learn the fluorescent asbestos morphologies. The mean average precision at a threshold of 0.5 ([email protected]) was 96.1% ± 0.4%, using the National Institute for Occupational Safety and Health (NIOSH) fiber counting Method 7400 as a reference method. Compared to our previous counting software (Intec/HU), the YOLOv4 achieved higher accuracy (0.997 vs. 0.979), particularly much higher precision (0.898 vs. 0.418), recall (0.898 vs. 0.780) and F-1 score (0.898 vs. 0.544). In addition, the YOLOv4 performed much better for low fiber concentration samples (<15 fibers/liter) compared to Intec/HU. Therefore, the FM method coupled with YOLOv4 is remarkable in detecting asbestos fibers and differentiating them from other non-asbestos particles.


Author(s):  
Mohamed Estai ◽  
Marc Tennant ◽  
Dieter Gebauer ◽  
Andrew Brostek ◽  
Janardhan Vignarajan ◽  
...  

Objective: This study aimed to evaluate an automated detection system to detect and classify permanent teeth on orthopantomogram (OPG) images using convolutional neural networks (CNNs). Methods: In total, 591 digital OPGs were collected from patients older than 18 years. Three qualified dentists performed individual teeth labelling on images to generate the ground truth annotations. A three-step procedure, relying upon CNNs, was proposed for automated detection and classification of teeth. Firstly, U-Net, a type of CNN, performed preliminary segmentation of tooth regions or detecting regions of interest (ROIs) on panoramic images. Secondly, the Faster R-CNN, an advanced object detection architecture, identified each tooth within the ROI determined by the U-Net. Thirdly, VGG-16 architecture classified each tooth into 32 categories, and a tooth number was assigned. A total of 17,135 teeth cropped from 591 radiographs were used to train and validate the tooth detection and tooth numbering modules. 90% of OPG images were used for training, and the remaining 10% were used for validation. 10-folds cross-validation was performed for measuring the performance. The intersection over union (IoU), F1 score, precision, and recall (i.e. sensitivity) were used as metrics to evaluate the performance of resultant CNNs. Results: The ROI detection module had an IoU of 0.70. The tooth detection module achieved a recall of 0.99 and a precision of 0.99. The tooth numbering module had a recall, precision and F1 score of 0.98. Conclusion: The resultant automated method achieved high performance for automated tooth detection and numbering from OPG images. Deep learning can be helpful in the automatic filing of dental charts in general dentistry and forensic medicine.


Author(s):  
Ryan Lagerquist ◽  
Jebb Q. Stewart ◽  
Imme Ebert-Uphoff ◽  
Christina Kumler

AbstractPredicting the timing and location of thunderstorms (“convection”) allows for preventive actions that can save both lives and property. We have applied U-nets, a deep-learning-based type of neural network, to forecast convection on a grid at lead times up to 120 minutes. The goal is to make skillful forecasts with only present and past satellite data as predictors. Specifically, predictors are multispectral brightness-temperature images from the Himawari-8 satellite, while targets (ground truth) are provided by weather radars in Taiwan. U-nets are becoming popular in atmospheric science due to their advantages for gridded prediction. Furthermore, we use three novel approaches to advance U-nets in atmospheric science. First, we compare three architectures – vanilla, temporal, and U-net++ – and find that vanilla U-nets are best for this task. Second, we train U-nets with the fractions skill score, which is spatially aware, as the loss function. Third, because we do not have adequate ground truth over the full Himawari-8 domain, we train the U-nets with small radar-centered patches, then apply trained U-nets to the full domain. Also, we find that the best predictions are given by U-nets trained with satellite data from multiple lag times, not only the present. We evaluate U-nets in detail – by time of day, month, and geographic location – and compare to persistence models. The U-nets outperform persistence at lead times ≥ 60 minutes, and at all lead times the U-nets provide a more realistic climatology than persistence. Our code is available publicly.


Author(s):  
Artem Nikonorov ◽  
Maksim Petrov ◽  
Sergey Bibikov ◽  
Viktoria Kutikova ◽  
Pavel Yakimov ◽  
...  

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