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Register a new userNeural Network Segmentation of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis in Renal Biopsies
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Brandon Ginley
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Glomerulosclerosis, interstitial fibrosis, and tubular atrophy (IFTA) are histologic indicators of irrecoverable kidney injury. In standard clinical practice, the renal pathologist visually assesses, under the microscope, the percentage of sclerotic glomeruli and the percentage of renal cortical involvement by IFTA. Estimation of IFTA is a subjective process due to a varied spectrum and definition of morphological manifestations. Modern artificial intelligence and computer vision algorithms have the ability to reduce inter-observer variability through rigorous quantitation. In this work, we apply convolutional neural networks for the segmentation of glomerulosclerosis and IFTA in periodic acid-Schiff stained renal biopsies. The convolutional network approach achieves high performance in intra-institutional holdout data, and achieves moderate performance in inter-intuitional holdout data, which the network had never seen in training. The convolutional approach demonstrated interesting properties, such as learning to predict regions better than the provided ground truth as well as developing its own conceptualization of segmental sclerosis. Subsequent estimations of IFTA and glomerulosclerosis percentages showed high correlation with ground truth.
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We present a proof-of-concept, deep learning (DL) based, differentiable biomechanical model of realistic brain deformations. Using prescribed maps of local atrophy and growth as input, the network learns to deform images according to a Neo-Hookean model of tissue deformation. The tool is validated using longitudinal brain atrophy data from the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset, and we demonstrate that the trained model is capable of rapidly simulating new brain deformations with minimal residuals. This method has the potential to be used in data augmentation or for the exploration of different causal hypotheses reflecting brain growth and atrophy.
Renal compartment segmentation on CT images targets on extracting the 3D structure of renal compartments from abdominal CTA images and is of great significance to the diagnosis and treatment for kidney diseases. However, due to the unclear compartment boundary, thin compartment structure and large anatomy variation of 3D kidney CT images, deep-learning based renal compartment segmentation is a challenging task. We propose a novel weakly supervised learning framework, Cycle Prototype Network, for 3D renal compartment segmentation. It has three innovations: 1) A Cycle Prototype Learning (CPL) is proposed to learn consistency for generalization. It learns from pseudo labels through the forward process and learns consistency regularization through the reverse process. The two processes make the model robust to noise and label-efficient. 2) We propose a Bayes Weakly Supervised Module (BWSM) based on cross-period prior knowledge. It learns prior knowledge from cross-period unlabeled data and perform error correction automatically, thus generates accurate pseudo labels. 3) We present a Fine Decoding Feature Extractor (FDFE) for fine-grained feature extraction. It combines global morphology information and local detail information to obtain feature maps with sharp detail, so the model will achieve fine segmentation on thin structures. Our model achieves Dice of 79.1% and 78.7% with only four labeled images, achieving a significant improvement by about 20% than typical prototype model PANet.
Objective: Interstitial fluid flow through vascular adventitia has been disclosed recently. However, its kinetic pattern was unclear. Methods and Results: We used histological and topographical identifications to observe ISF flow along venous vessels in rabbits. By MRI in alive subjects, the inherent ISF flow pathways in legs, abdomen and thorax were enhanced by paramagnetic contrast from ankle dermis. By fluorescence stereomicroscopy and layer-by-layer dissection after the rabbits were sacrificed, the perivascular and adventitial connective tissues (PACT) along the saphenous veins and inferior vena cava were found to be stained by sodium fluorescein from ankle dermis, which coincided with the findings by MRI. By confocal microscopy and histological analysis, the stained PACT pathways were verified to be the fibrous connective tissues and consisted of longitudinally assembled fibers. By usages of nanoparticles and surfactants, a PACT pathway was found to be accessible for a nanoparticle under 100nm and contain two parts: a tunica channel part and an absorptive part. In real-time observations, the calculated velocity of a continuous ISF flow along fibers of a PACT pathway was 3.6-15.6 mm/sec. Conclusion: These data further revealed more kinetic features of a continuous ISF flow along vascular vessel. A multiscale, multilayer, and multiform interstitial/interfacial fluid flow throughout perivascular and adventitial connective tissues was suggested as one of kinetic and dynamic mechanisms for ISF flow, which might be another principal fluid dynamic pattern besides convective/vascular and diffusive transport in biological system.
Background: The detection of perineural invasion (PNI) by carcinoma in prostate biopsies has been shown to be associated with poor prognosis. The assessment and quantification of PNI is; however, labor intensive. In the study we aimed to develop an algorithm based on deep neural networks to aid pathologists in this task. Methods: We collected, digitized and pixel-wise annotated the PNI findings in each of the approximately 80,000 biopsy cores from the 7,406 men who underwent biopsy in the prospective and diagnostic STHLM3 trial between 2012 and 2014. In total, 485 biopsy cores showed PNI. We also digitized more than 10% (n=8,318) of the PNI negative biopsy cores. Digitized biopsies from a random selection of 80% of the men were used to build deep neural networks, and the remaining 20% were used to evaluate the performance of the algorithm. Results: For the detection of PNI in prostate biopsy cores the network had an estimated area under the receiver operating characteristics curve of 0.98 (95% CI 0.97-0.99) based on 106 PNI positive cores and 1,652 PNI negative cores in the independent test set. For the pre-specified operating point this translates to sensitivity of 0.87 and specificity of 0.97. The corresponding positive and negative predictive values were 0.67 and 0.99, respectively. For localizing the regions of PNI within a slide we estimated an average intersection over union of 0.50 (CI: 0.46-0.55). Conclusion: We have developed an algorithm based on deep neural networks for detecting PNI in prostate biopsies with apparently acceptable diagnostic properties. These algorithms have the potential to aid pathologists in the day-to-day work by drastically reducing the number of biopsy cores that need to be assessed for PNI and by highlighting regions of diagnostic interest.
We seek to investigate the scalability of neuromorphic computing for computer vision, with the objective of replicating non-neuromorphic performance on computer vision tasks while reducing power consumption. We convert the deep Artificial Neural Network (ANN) architecture U-Net to a Spiking Neural Network (SNN) architecture using the Nengo framework. Both rate-based and spike-based models are trained and optimized for benchmarking performance and power, using a modified version of the ISBI 2D EM Segmentation dataset consisting of microscope images of cells. We propose a partitioning method to optimize inter-chip communication to improve speed and energy efficiency when deploying multi-chip networks on the Loihi neuromorphic chip. We explore the advantages of regularizing firing rates of Loihi neurons for converting ANN to SNN with minimum accuracy loss and optimized energy consumption. We propose a percentile based regularization loss function to limit the spiking rate of the neuron between a desired range. The SNN is converted directly from the corresponding ANN, and demonstrates similar semantic segmentation as the ANN using the same number of neurons and weights. However, the neuromorphic implementation on the Intel Loihi neuromorphic chip is over 2x more energy-efficient than conventional hardware (CPU, GPU) when running online (one image at a time). These power improvements are achieved without sacrificing the task performance accuracy of the network, and when all weights (Loihi, CPU, and GPU networks) are quantized to 8 bits.
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