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Front Matter: Volume 10140

Proceedings of SPIE, Metin N. Gurcan, John E. Tomaszewski
2017 Medical Imaging 2017: Digital Pathology  
using a Base 36 numbering system employing both numerals and letters.  ...  Publication of record for individual papers is online in the SPIE Digital Library. Paper Numbering: Proceedings of SPIE follow an e-First publication model.  ...  Color normalization of histology slides using graph regularized sparse NMF [10140-37] 10140 11 Frequency analysis of gaze points with CT colonography interpretation using eye gaze tracking system [  ... 
doi:10.1117/12.2270372 dblp:conf/midp/X17 fatcat:6yeb63ix6bau7jhipthayjih24

Connectional architecture of the prefrontal cortex in the marmoset brain [article]

Akiya Watakabe, Henrik Skibbe, Ken Nakae, Hiroshi Abe, Noritaka Ichinohe, Jian Wang, Masafumi Takaji, Hiroaki Mizukami, Alexander Woodward, Rui Gong, Junichi Hata, Hideyuki Okano (+2 others)
2021 bioRxiv   pre-print
of several common motifs representing the framework of PFC connectivity.  ...  Based on connectomics mapping of the marmoset PFC, we characterized two contrasting features of corticocortical and corticostriatal projections.  ...  The colors of the bar graphs indicate the DL, ML, and UL types. The areal distribution shows the overlay of all samples, and the bar graphs show the average values per injection.  ... 
doi:10.1101/2021.12.26.474213 fatcat:qjljvxrqnrez5aey6ke2yp7gvq

Multi-omics Data Integration, Interpretation, and Its Application

Indhupriya Subramanian, Srikant Verma, Shiva Kumar, Abhay Jere, Krishanpal Anamika
2020 Bioinformatics and Biology Insights  
We provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration  ...  With the advent of high-throughput techniques and availability of multi-omics data generated from a large set of samples, several promising tools and methods have been developed for data integration and  ...  We thank the anonymous reviewers for their useful comments and valuable suggestions.  ... 
doi:10.1177/1177932219899051 pmid:32076369 pmcid:PMC7003173 fatcat:dchnmbmzh5di7jcuc7ilxjsk3e

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Adam Abeshouse, Clement Adebamowo, Sally N. Adebamowo, Rehan Akbani, Teniola Akeredolu, Adrian Ally, Matthew L. Anderson, Pavana Anur, Elizabeth L. Appelbaum, Joshua Armenia, J. Todd Auman, Matthew H. Bailey (+252 others)
2017 Cell  
Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity.  ...  We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types.  ...  Color was normalized to a standard H&E image using Reinhard color normalization that maps the LAB color space statistics of each image to the standard to improve the analysis consistency.  ... 
doi:10.1016/j.cell.2017.10.014 pmid:29100075 pmcid:PMC5693358 fatcat:xq7ald3qf5fixolsmscmuda2yq

Classification of Breast Cancer Histopathological Images Using Discriminative Patches Screened by Generative Adversarial Networks

Rui Man, Ping Yang, Bowen Xu
2020 IEEE Access  
It transforms the stain separation prob-lem into a non-negative matrix factorization (NMF) [42] to which we add a sparseness constraint, which is called sparse non-negative matrix factorization (SNMF  ...  [16] also considered to segment the epithelial layer around the cell cavity by using the spatio-color-texture graph, and statistical texture features were used to train the final classifier.  ...  Note that "Res" refers to resizing original images to a new size, "DA" refers to data augmentation, "Rot" refers to rotation, "Flip" refers to flipping, "SN" refers to stain normalization.  ... 
doi:10.1109/access.2020.3019327 fatcat:67sqnbrzynehlo5mwwnwtoz4ra

Cancer Diagnosis Using Deep Learning: A Bibliographic Review

Khushboo Munir, Hassan Elahi, Afsheen Ayub, Fabrizio Frezza, Antonello Rizzi
2019 Cancers  
In this paper, we first describe the basics of the field of cancer diagnosis, which includes steps of cancer diagnosis followed by the typical classification methods used by doctors, providing a historical  ...  These methods include Asymmetry, Border, Color and Diameter (ABCD) method, seven-point detection method, Menzies method, and pattern analysis.  ...  A deep cascade network was proposed for the detection of mitosis from the breast histology slides [85] . From the histology slides, the mitosis candidates were extracted using the trained FCN model.  ... 
doi:10.3390/cancers11091235 pmid:31450799 pmcid:PMC6770116 fatcat:ktuuttdu6zc7phj3mahp5yynxq

Investigations into the causes of early larval mortality in cultured summer flounder (Paralichthys dentatus L.)

David Alves, Jennifer L Specker, David A Bengtson
1999 Aquaculture  
Wolke, who -always had good suggestions and were more than generous in allowing me use of their laboratories and access to the expertise of the people in their labs.  ...  Larvae were raised in 2-L bowls at initial densities of 50 and 75/L with light aeration, 12L:12D photoperiod, and regular 1-L water changes.  ...  fish culture is a determination of what is normal, viz the morphology of the larvae.  ... 
doi:10.1016/s0044-8486(99)00058-7 fatcat:64gchl5bqbap3cliorkbjfhkc4

Tools for Automated Histology Image Analysis

Michael T. McCann
While slide preparation and imaging is increasingly becoming automated, the analysis of the resulting histology images is not: even routine analyses still require the trained eyes of a pathologist.  ...  Our first contribution is in the area of histology image normalization, where the goal is to digitally remove the variation in staining between histology images, an important preprocessing step in many  ...  We compare our two algorithms to five others: Normalized Cut [7] forms a graph from an image by using pixels as nodes and assigning edge weights based on distance and color similarity.  ... 
doi:10.1184/r1/6723926.v1 fatcat:ok2qiqfa3nbxjocmzdzrw555ym

DeepHealth: Review and challenges of artificial intelligence in health informatics [article]

Gloria Hyunjung Kwak, Pan Hui
2020 arXiv   pre-print
Artificial intelligence has provided us with an exploration of a whole new research era.  ...  , feasibility, security, scalability) for practical use.  ...  Several variants exist to the basic model, forcing learned representations of input to assume useful features, which are regularized autoencoders (sparse, denoising, stacked denoising, and contractive  ... 
arXiv:1909.00384v2 fatcat:sy7pm2c2uvdd3pal2russn4xri

Eleven grand challenges in single-cell data science

David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums (+39 others)
2020 Genome Biology  
Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward.  ...  Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems.  ...  Imputation methods could therefore be used for normalization, but do not entail all possible or useful approaches to normalization.  ... 
doi:10.1186/s13059-020-1926-6 pmid:32033589 pmcid:PMC7007675 fatcat:cebolwlnmfbh3fdyrq75kgbrm4

Discovery of Latent Factors in High-dimensional Data Using Tensor Methods [article]

Furong Huang
2016 arXiv   pre-print
This thesis presents theoretical results on convergence to globally optimal solution of tensor decomposition using the stochastic gradient descent, despite non-convexity of the objective.  ...  My thesis spans both theoretical analysis of tensor decomposition framework and practical implementation of various applications.  ...  hand, the sparse implementation on CPU is fast and memory efficient in the case of sparse graphs with a small number of communities while the dense implementation on GPU is faster for denser graphs such  ... 
arXiv:1606.03212v1 fatcat:j2nlv4fpyvbfjidutiofteuu4u

Molecular dissection of the oncogenic role of ETS1 in the mesenchymal subtypes of head and neck squamous cell carcinoma

Christian Gluck, Alexandra Glathar, Maria Tsompana, Norma Nowak, Lee Ann Garrett-Sinha, Michael J. Buck, Satrajit Sinha, Peter Hammerman
2019 PLoS Genetics  
Recent genomic analysis of HNSCC tumors has identified several distinct molecular classes, of which the mesenchymal subtype is associated with Epithelial to Mesenchymal Transition (EMT) and shown to correlate  ...  Head and Neck Squamous Cell Carcinoma (HNSCC) is a heterogeneous disease of significant mortality and with limited treatment options.  ...  William Kaelin for the gift of the ETS1 and control shRNA lentiviral plasmids. We thank Kirsten Smalley for excellent technical help and Dr. Rose-Anne Romano for critical reading of the manuscript.  ... 
doi:10.1371/journal.pgen.1008250 pmid:31306413 pmcid:PMC6657958 fatcat:vdjd6na7rvctpbzmkf2giun3vi

CARS 2021: Computer Assisted Radiology and Surgery Proceedings of the 35th International Congress and Exhibition Munich, Germany, June 21–25, 2021

2021 International Journal of Computer Assisted Radiology and Surgery  
Methods We used the digital 8-bit ultrasound images of 107 histologically proven (53 malignant and 54 benign, without regard to their histological subtype) breast lesions obtained with the help of the  ...  The similarity metric function can be mean square error (MSE) or normalized crosscorrelation (NCC). And the smooth regularization function works on the gradients of deformable field.  ... 
doi:10.1007/s11548-021-02375-4 pmid:34085172 fatcat:6d564hsv2fbybkhw4wvc7uuxcy

Self-Organized Evolutionary Process in Sets of Interdependent Variables near the Midpoint of Phase Transition in K-Satisfiability [chapter]

Michael Korkin
2001 Lecture Notes in Computer Science  
During the normal aging process in the prostate a variety of histologic changes are seen including regions termed inflammatory atrophy where mononuclear infiltrating cells are seen adjacent to atrophic  ...  It uses normalized cross-correlation of grey levels in variable sized chips for image matching.  ... 
doi:10.1007/3-540-45443-8_20 fatcat:ght26tu6avh57kkp54kifofaee

Abstracts OAS

2019 Allergy. European Journal of Allergy and Clinical Immunology  
All pregnant patients had normal pregnancy outcomes and delivered healthy infants.  ...  Outcomes were compared using generalized logistic regression models.  ...  and regular use of topical corticosteroids and/or moisturisers).  ... 
doi:10.1111/all.13957 pmid:31396968 fatcat:u2sqfatubbgqpeg2ph4klfhqiq
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