Deep Learning-Based Nuclei Segmentation of Cleared Brain Tissue

2019 ◽  
Author(s):  
Pooya Khorrami ◽  
Kevin Brady ◽  
Mark Hernandez ◽  
Lars Gjesteby ◽  
Sara N. Burke ◽  
...  
Keyword(s):  
Deep Learning ◽  
Brain Tissue ◽  
Nuclei Segmentation

scholarly journals Development of deep learning models for microglia analyses in brain tissue using DeePathology™ STUDIO

2021 ◽  
pp. 109371
Author(s):  
Luisa Möhle ◽  
Pablo Bascuñana ◽  
Mirjam Brackhan ◽  
Jens Pahnke
Keyword(s):  
Deep Learning ◽  
Brain Tissue ◽  
Learning Models

scholarly journals Deep learning from MRI-derived labels enables automatic brain tissue classification on human brain CT

NeuroImage ◽  
2021 ◽  
pp. 118606
Author(s):  
Meera Srikrishna ◽  
Joana B. Pereira ◽  
Rolf A. Heckemann ◽  
Giovanni Volpe ◽  
Danielle van Westen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Human Brain ◽  
Brain Tissue ◽  
Tissue Classification ◽  
Brain Ct

scholarly journals Enhancing Multi-tissue and Multi-scale Cell Nuclei Segmentation with Deep Metric Learning

2020 ◽  
Vol 10 (2) ◽  
pp. 615 ◽  
Author(s):  
Tomas Iesmantas ◽  
Agne Paulauskaite-Taraseviciene ◽  
Kristina Sutiene
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Metric Learning ◽  
Cell Nuclei ◽  
Similarity Coefficients ◽  
Clinical Practices ◽  
Nuclei Segmentation ◽  
Wide Range ◽  
Triplet Loss ◽  
Deep Metric Learning

(1) Background: The segmentation of cell nuclei is an essential task in a wide range of biomedical studies and clinical practices. The full automation of this process remains a challenge due to intra- and internuclear variations across a wide range of tissue morphologies, differences in staining protocols and imaging procedures. (2) Methods: A deep learning model with metric embeddings such as contrastive loss and triplet loss with semi-hard negative mining is proposed in order to accurately segment cell nuclei in a diverse set of microscopy images. The effectiveness of the proposed model was tested on a large-scale multi-tissue collection of microscopy image sets. (3) Results: The use of deep metric learning increased the overall segmentation prediction by 3.12% in the average value of Dice similarity coefficients as compared to no metric learning. In particular, the largest gain was observed for segmenting cell nuclei in H&E -stained images when deep learning network and triplet loss with semi-hard negative mining were considered for the task. (4) Conclusion: We conclude that deep metric learning gives an additional boost to the overall learning process and consequently improves the segmentation performance. Notably, the improvement ranges approximately between 0.13% and 22.31% for different types of images in the terms of Dice coefficients when compared to no metric deep learning.

Deep learning-based nuclei segmentation and classification in histopathology images with application to imaging genomics

2021 ◽  
pp. 185-201
Author(s):  
Dimitris Metaxas ◽  
Hui Qu ◽  
Gregory Riedlinger ◽  
Pengxiang Wu ◽  
Qiaoying Huang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Imaging Genomics ◽  
Nuclei Segmentation ◽  
Histopathology Images

scholarly journals Efficient Stain-Aware Nuclei Segmentation Deep Learning Framework for Multi-Center Histopathological Images

Electronics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 954
Author(s):  
Loay Hassan ◽  
Mohamed Abdel-Nasser ◽  
Adel Saleh ◽  
Osama A. Omer ◽  
Domenec Puig
Keyword(s):  
Deep Learning ◽  
Choquet Integral ◽  
Adjacent Cell ◽  
Cell Nuclei ◽  
Nuclei Segmentation ◽  
Learning Framework ◽  
Segmentation Methods ◽  
Histopathological Images ◽  
The Individual ◽  
Whole Slide Images

Existing nuclei segmentation methods have obtained limited results with multi-center and multi-organ whole-slide images (WSIs) due to the use of different stains, scanners, overlapping, clumped nuclei, and the ambiguous boundary between adjacent cell nuclei. In an attempt to address these problems, we propose an efficient stain-aware nuclei segmentation method based on deep learning for multi-center WSIs. Unlike all related works that exploit a single-stain template from the dataset to normalize WSIs, we propose an efficient algorithm to select a set of stain templates based on stain clustering. Individual deep learning models are trained based on each stain template, and then, an aggregation function based on the Choquet integral is employed to combine the segmentation masks of the individual models. With a challenging multi-center multi-organ WSIs dataset, the experimental results demonstrate that the proposed method outperforms the state-of-art nuclei segmentation methods with aggregated Jaccard index (AJI) and F1-scores of 73.23% and 89.32%, respectively, while achieving a lower number of parameters.

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