scholarly journals Discrete Protein Metric (DPM): A new image similarity metric to calculate accuracy of deep learning-generated cell focal adhesion predictions

2021 ◽  
Author(s):  
Miguel Alejandro Contreras ◽  
William Bachman ◽  
David S Long
Keyword(s):  
Deep Learning ◽  
Focal Adhesion ◽  
Pearson Correlation ◽  
Similarity Index ◽  
Ground Truth ◽  
Image Similarity ◽  
Point Pattern ◽  
Accuracy Score ◽  
Site Location ◽  
Similarity Metric

Understanding cell behaviors can provide new knowledge on the development of different pathologies. Focal adhesion (FA) sites are important sub-cellular structures that are involved in these processes. To better facilitate the study of FA sites, deep learning (DL) can be used to predict FA site morphology based on limited datasets (e.g., cell membrane images). However, calculating the accuracy score of these predictions can be challenging due to the discrete/point pattern like nature of FA sites. In the present work, a new image similarity metric, discrete protein metric (DPM), was developed to calculate FA prediction accuracy. This metric measures differences in distribution (d), shape/size (s), and angle (a) of FA sites between the predicted image and its ground truth image. Performance of the DPM was evaluated by comparing it to three other commonly used image similarity metrics: Pearson correlation coefficient (PCC), feature similarity index (FSIM), and Intersection over Union (IoU). A sensitivity analysis was performed by comparing changes in each metric value due to quantifiable changes in FA site location, number, aspect ratio, area, or orientation. Furthermore, accuracy score of DL-generated predictions was calculated using all four metrics to compare their ability to capture variation across samples. Results showed better sensitivity and range of variation for DPM compared to the other metrics tested. Most importantly, DPM had the ability to determine which FA predictions were quantitatively more accurate and consistent with qualitative assessments. The proposed DPM hence provides a method to validate DL-generated FA predictions and can be extended to evaluating other predicted or segmented discrete structures of biomedical relevance.

scholarly journals Franken-CT: Head and Neck MR-Based Pseudo-CT Synthesis Using Diverse Anatomical Overlapping MR-CT Scans

2021 ◽  
Vol 11 (8) ◽  
pp. 3508
Author(s):  
Pedro Miguel Martinez-Girones ◽  
Javier Vera-Olmos ◽  
Mario Gil-Correa ◽  
Ana Ramos ◽  
Lina Garcia-Cañamaque ◽  
...  
Keyword(s):  
Deep Learning ◽  
Confidence Interval ◽  
Head And Neck ◽  
Similarity Index ◽  
Ground Truth ◽  
Structural Similarity ◽  
Absolute Error ◽  
Ct Scans ◽  
Learning Methods ◽  
Index Measure

Typically, pseudo-Computerized Tomography (CT) synthesis schemes proposed in the literature rely on complete atlases acquired with the same field of view (FOV) as the input volume. However, clinical CTs are usually acquired in a reduced FOV to decrease patient ionization. In this work, we present the Franken-CT approach, showing how the use of a non-parametric atlas composed of diverse anatomical overlapping Magnetic Resonance (MR)-CT scans and deep learning methods based on the U-net architecture enable synthesizing extended head and neck pseudo-CTs. Visual inspection of the results shows the high quality of the pseudo-CT and the robustness of the method, which is able to capture the details of the bone contours despite synthesizing the resulting image from knowledge obtained from images acquired with a completely different FOV. The experimental Zero-Normalized Cross-Correlation (ZNCC) reports 0.9367 ± 0.0138 (mean ± SD) and 95% confidence interval (0.9221, 0.9512); the experimental Mean Absolute Error (MAE) reports 73.9149 ± 9.2101 HU and 95% confidence interval (66.3383, 81.4915); the Structural Similarity Index Measure (SSIM) reports 0.9943 ± 0.0009 and 95% confidence interval (0.9935, 0.9951); and the experimental Dice coefficient for bone tissue reports 0.7051 ± 0.1126 and 95% confidence interval (0.6125, 0.7977). The voxel-by-voxel correlation plot shows an excellent correlation between pseudo-CT and ground-truth CT Hounsfield Units (m = 0.87; adjusted R2 = 0.91; p < 0.001). The Bland–Altman plot shows that the average of the differences is low (−38.6471 ± 199.6100; 95% CI (−429.8827, 352.5884)). This work serves as a proof of concept to demonstrate the great potential of deep learning methods for pseudo-CT synthesis and their great potential using real clinical datasets.

scholarly journals Deep Learning Based Super Resolution and Classification Applications for Neonatal Thermal Images

2021 ◽  
Vol 38 (5) ◽  
pp. 1361-1368
Author(s):  
Fatih M. Senalp ◽  
Murat Ceylan
Keyword(s):  
Deep Learning ◽  
High Resolution ◽  
Thermal Imaging ◽  
Similarity Index ◽  
Super Resolution ◽  
Ground Truth ◽  
Structural Similarity ◽  
Generative Adversarial Networks ◽  
Thermal Camera ◽  
Thermal Images

The thermal camera systems can be used in all kinds of applications that require the detection of heat change, but thermal imaging systems are highly costly systems. In recent years, developments in the field of deep learning have increased the success by obtaining quality results compared to traditional methods. In this paper, thermal images of neonates (healthy - unhealthy) obtained from a high-resolution thermal camera were used and these images were evaluated as high resolution (ground truth) images. Later, these thermal images were downscaled at 1/2, 1/4, 1/8 ratios, and three different datasets consisting of low-resolution images in different sizes were obtained. In this way, super-resolution applications have been carried out on the deep network model developed based on generative adversarial networks (GAN) by using three different datasets. The successful performance of the results was evaluated with PSNR (peak signal to noise ratio) and SSIM (structural similarity index measure). In addition, healthy - unhealthy classification application was carried out by means of a classifier network developed based on convolutional neural networks (CNN) to evaluate the super-resolution images obtained using different datasets. The obtained results show the importance of combining medical thermal imaging with super-resolution methods.

Computed Tomography Perfusion–Based Prediction of Core Infarct and Tissue at Risk: Can Artificial Intelligence Help Reduce Radiation Exposure?

Stroke ◽  
2021 ◽  
Author(s):  
Girish Bathla ◽  
Yanan Liu ◽  
Honghai Zhang ◽  
Milan Sonka ◽  
Colin Derdeyn
Keyword(s):  
Artificial Intelligence ◽  
Pearson Correlation ◽  
Similarity Index ◽  
Ground Truth ◽  
Structural Similarity ◽  
Data Sets ◽  
Structural Similarity Index ◽  
Computed Tomographic ◽  
Index Measure ◽  
Core Infarct

Background and Purpose: We explored the feasibility of automated, arterial input function independent, vendor neutral prediction of core infarct, and penumbral tissue using complete and partial computed tomographic perfusion data sets through neural networks. Methods: Using retrospective computed tomographic perfusion data from 57 patients, split as training/validation (60%/40%), we developed and validated separate 2-dimensional U-net models for cerebral blood flow (CBF) and time to maximum (Tmax) maps calculation to predict core infarct and tissue at risk, respectively. Once trained, the full sets of 28 input images were sequentially reduced to equitemporal 14, 10, and 7 time points. The averaged structural similarity index measure between the model-derived images and ground truth perfusion maps was compared. Volumes for core infarct and Tmax were compared using the Pearson correlation coefficient. Results: Both CBF and Tmax maps derived using 28 and 14 time points had similar structural similarity index measure (0.80–0.81; P >0.05) when compared with ground truth images. The Pearson correlation for the CBF and Tmax volumes derived from the model using 28-tp with ground truth volumes derived from the RAPID software was 0.69 for CBF and 0.74 for Tmax. The predicted maps were fully concordant in terms of laterality to the commercial perfusion maps. The mean Dice scores were 0.54 for the core infarct and 0.63 for the hypoperfusion maps. Conclusion: Artificial intelligence model-derived volumes show good correlation with RAPID-derived volumes for CBF and Tmax. Within the constraints of a small sample size, the perfusion map quality is similar when using 14-tp instead of 28-tp. Our findings provide proof of concept that vendor neutral artificial intelligence models for computed tomographic perfusion processing using complete or partial image data sets appear feasible. The model accuracy could be further optimized using larger data sets.

scholarly journals Fourier Ring Correlation and Anisotropic Kernel Density Estimation Improve Deep Learning Based SMLM Reconstruction of Microtubules

2021 ◽  
Vol 1 ◽  
Author(s):  
Andreas Berberich ◽  
Andreas Kurz ◽  
Sebastian Reinhard ◽  
Torsten Johann Paul ◽  
Paul Ray Burd ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Similarity Index ◽  
Kernel Density ◽  
Ground Truth ◽  
Quality Measure ◽  
Gaussian Kernel ◽  
Limiting Factor ◽  
Density Estimator

Single-molecule super-resolution microscopy (SMLM) techniques like dSTORM can reveal biological structures down to the nanometer scale. The achievable resolution is not only defined by the localization precision of individual fluorescent molecules, but also by their density, which becomes a limiting factor e.g., in expansion microscopy. Artificial deep neural networks can learn to reconstruct dense super-resolved structures such as microtubules from a sparse, noisy set of data points. This approach requires a robust method to assess the quality of a predicted density image and to quantitatively compare it to a ground truth image. Such a quality measure needs to be differentiable to be applied as loss function in deep learning. We developed a new trainable quality measure based on Fourier Ring Correlation (FRC) and used it to train deep neural networks to map a small number of sampling points to an underlying density. Smooth ground truth images of microtubules were generated from localization coordinates using an anisotropic Gaussian kernel density estimator. We show that the FRC criterion ideally complements the existing state-of-the-art multiscale structural similarity index, since both are interpretable and there is no trade-off between them during optimization. The TensorFlow implementation of our FRC metric can easily be integrated into existing deep learning workflows.

ANALISIS SENSITIVITAS VIDEO MPEG-4 BERDASARKAN STRUKTUR FRAME PADA TRANSMISI DVB-T

2020 ◽  
Vol 25 (2) ◽  
pp. 86-97
Author(s):  
Sandy Suryo Prayogo ◽  
Tubagus Maulana Kusuma
Keyword(s):  
Deep Learning ◽  
Bit Error Rate ◽  
Error Rate ◽  
Signal To Noise Ratio ◽  
Similarity Index ◽  
Structural Similarity ◽  
Signal To Noise ◽  
Structural Similarity Index ◽  
Noise Ratio

DVB merupakan standar transmisi televisi digital yang paling banyak digunakan saat ini. Unsur terpenting dari suatu proses transmisi adalah kualitas gambar dari video yang diterima setelah melalui proses transimisi tersebut. Banyak faktor yang dapat mempengaruhi kualitas dari suatu gambar, salah satunya adalah struktur frame dari video. Pada tulisan ini dilakukan pengujian sensitifitas video MPEG-4 berdasarkan struktur frame pada transmisi DVB-T. Pengujian dilakukan menggunakan simulasi matlab dan simulink. Digunakan juga ffmpeg untuk menyediakan format dan pengaturan video akan disimulasikan. Variabel yang diubah dari video adalah bitrate dan juga group-of-pictures (GOP), sedangkan variabel yang diubah dari transmisi DVB-T adalah signal-to-noise-ratio (SNR) pada kanal AWGN di antara pengirim (Tx) dan penerima (Rx). Hasil yang diperoleh dari percobaan berupa kualitas rata-rata gambar pada video yang diukur menggunakan metode pengukuran structural-similarity-index (SSIM). Dilakukan juga pengukuran terhadap jumlah bit-error-rate BER pada bitstream DVB-T. Percobaan yang dilakukan dapat menunjukkan seberapa besar sensitifitas bitrate dan GOP dari video pada transmisi DVB-T dengan kesimpulan semakin besar bitrate maka akan semakin buruk nilai kualitas gambarnya, dan semakin kecil nilai GOP maka akan semakin baik nilai kualitasnya. Penilitian diharapkan dapat dikembangkan menggunakan deep learning untuk memperoleh frame struktur yang tepat di kondisi-kondisi tertentu dalam proses transmisi televisi digital.

scholarly journals Spectroscopic and deep learning-based approaches to identify and quantify cerebral microhemorrhages

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Crouzet ◽  
Gwangjin Jeong ◽  
Rachel H. Chae ◽  
Krystal T. LoPresti ◽  
Cody E. Dunn ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prussian Blue ◽  
Processing Speed ◽  
Digital Pathology ◽  
Ground Truth ◽  
Individual Variability ◽  
Rgb Images ◽  
Cerebral Microhemorrhages ◽  
Phasor Analysis ◽  
Better Than

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.

scholarly journals Fully Data-Driven Pseudohealthy Synthesis for Planning Valve-Sparing Aortic Root Reconstruction using Conditional Variational Autoencoders

2020 ◽  
Vol 6 (3) ◽  
pp. 284-287
Author(s):  
Jannis Hagenah ◽  
Mohamad Mehdi ◽  
Floris Ernst
Keyword(s):  
Aortic Root ◽  
Similarity Index ◽  
Ground Truth ◽  
Representation Learning ◽  
Patient Specific ◽  
Ultrasound Images ◽  
Specific Geometry ◽  
The Individual ◽  
Native Root ◽  
Original Information

AbstractAortic root aneurysm is treated by replacing the dilated root by a grafted prosthesis which mimics the native root morphology of the individual patient. The challenge in predicting the optimal prosthesis size rises from the highly patient-specific geometry as well as the absence of the original information on the healthy root. Therefore, the estimation is only possible based on the available pathological data. In this paper, we show that representation learning with Conditional Variational Autoencoders is capable of turning the distorted geometry of the aortic root into smoother shapes while the information on the individual anatomy is preserved. We evaluated this method using ultrasound images of the porcine aortic root alongside their labels. The observed results show highly realistic resemblance in shape and size to the ground truth images. Furthermore, the similarity index has noticeably improved compared to the pathological images. This provides a promising technique in planning individual aortic root replacement.

scholarly journals Synthetic polarization-sensitive optical coherence tomography by deep learning

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yi Sun ◽  
Jianfeng Wang ◽  
Jindou Shi ◽  
Stephen A. Boppart
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
Imaging System ◽  
Imaging Modality ◽  
Similarity Index ◽  
Polarization Sensitivity ◽  
Imaging Method ◽  
Optical Coherence ◽  
The Real ◽  
Oct Imaging

AbstractPolarization-sensitive optical coherence tomography (PS-OCT) is a high-resolution label-free optical biomedical imaging modality that is sensitive to the microstructural architecture in tissue that gives rise to form birefringence, such as collagen or muscle fibers. To enable polarization sensitivity in an OCT system, however, requires additional hardware and complexity. We developed a deep-learning method to synthesize PS-OCT images by training a generative adversarial network (GAN) on OCT intensity and PS-OCT images. The synthesis accuracy was first evaluated by the structural similarity index (SSIM) between the synthetic and real PS-OCT images. Furthermore, the effectiveness of the computational PS-OCT images was validated by separately training two image classifiers using the real and synthetic PS-OCT images for cancer/normal classification. The similar classification results of the two trained classifiers demonstrate that the predicted PS-OCT images can be potentially used interchangeably in cancer diagnosis applications. In addition, we applied the trained GAN models on OCT images collected from a separate OCT imaging system, and the synthetic PS-OCT images correlate well with the real PS-OCT image collected from the same sample sites using the PS-OCT imaging system. This computational PS-OCT imaging method has the potential to reduce the cost, complexity, and need for hardware-based PS-OCT imaging systems.

scholarly journals IMG-22. A DEEP LEARNING MODEL FOR AUTOMATIC POSTERIOR FOSSA PEDIATRIC BRAIN TUMOR SEGMENTATION: A MULTI-INSTITUTIONAL STUDY

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii359-iii359
Author(s):  
Lydia Tam ◽  
Edward Lee ◽  
Michelle Han ◽  
Jason Wright ◽  
Leo Chen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Posterior Fossa ◽  
Ground Truth ◽  
Learning Model ◽  
Tumor Segmentation ◽  
Dice Similarity Coefficient ◽  
Study Cohort ◽  
Navigation Systems ◽  
Tumor Types ◽  
Deep Learning Model

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.

Patch-CNN: Deep learning for logo detection and brand recognition

2021 ◽  
pp. 1-14
Author(s):  
Waqas Yousaf ◽  
Arif Umar ◽  
Syed Hamad Shirazi ◽  
Zakir Khan ◽  
Imran Razzak ◽  
...  
Keyword(s):  
Deep Learning ◽  
Image Quality ◽  
Ground Truth ◽  
Logo Recognition ◽  
Brand Recognition ◽  
Detection And Recognition

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.

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