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Development of a novel 2D color map for interactive segmentation of histological images

Qaiser Chaudry, Yachna Sharma, Syed H. Raza, May D. Wang
2012 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)  
Our 2D color map interactive segmentation technique based on human color perception information and the color distribution of the input image, enables user control without noticeable delay.  ...  Our proposed method's results show good accuracy with low response and computational time making it a feasible method for user interactive applications involving segmentation of histological images.  ...  Young for providing us the imaging data and providing valuable information for interpretation of the results from pathological perspective. We would like to thank Dr. Richard Moffitt, Dr.  ... 
doi:10.1109/isbi.2012.6235513 pmid:28392890 pmcid:PMC5383090 dblp:conf/isbi/ChaudrySRW12 fatcat:3lxeddm47ndlpck6ddno57mof4

Multimodal Whole Brain Registration: MRI and High Resolution Histology

Maryana Alegro, Edson Amaro, Burlen Loring, Helmut Heinsen, Eduardo Alho, Lilla Zollei, Daniela Ushizima, Lea T. Grinberg
2016 2016 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)  
Multi-modal image registration: also very versatile allowing visualization of color images, matching mri with histology. SPIE, 7626, 2010. 2 surfaces, 2D and 3D objects in the same scene.  ...  We describe our pipeline and prelimi- histology correlation represents a breakthrough in explor- nary developments of scalable processing schemes for high- ing the neuronal basis of MRI  ... 
doi:10.1109/cvprw.2016.85 dblp:conf/cvpr/AlegroALHAZUG16 fatcat:izxuwskkybcx5i62badvy5z5ya

Whole mouse cryo-imaging

David Wilson, Debashish Roy, Grant Steyer, Madhusudhana Gargesha, Meredith Stone, Eliot McKinley, Xiaoping P. Hu, Anne V. Clough
2008 Medical Imaging 2008: Physiology, Function, and Structure from Medical Images  
The 3D results demonstrate the novel true-color volume visualization tools we have developed and the inherent advantage of cryo-imaging in providing unlimited depth of field and spatial resolution.  ...  The Case cryo-imaging system is a section and image system which allows one to acquire micronscale, information rich, whole mouse color bright field and molecular fluorescence images of an entire mouse  ...  ACKNOWLEDGMENT We acknowledge our collaborators for their valuable inputs and many of the specimens. The wild type mouse used to produce  ... 
doi:10.1117/12.772840 pmid:19756215 pmcid:PMC2743345 fatcat:pvzy7pw6m5el3mgbiyuikyaxla

Estimation of Pulmonary Motion in Healthy Subjects and Patients with Intrathoracic Tumors Using 3D-Dynamic MRI: Initial Results

Christian Plathow, Max Schoebinger, Felix Herth, Siegfried Tuengerthal, Heinz-Peter Meinzer, Hans-Ulrich Kauczor
2009 Korean Journal of Radiology  
An analysis of lung motion was performed and correlated with an established 2D-MRI technique for verification.  ...  Also, the vector color maps quantitatively illustrated regional lung motion in all healthy volunteers.  ...  The workflow for calculating dense vector fields from a 3D+t image sequence has been implemented in an interactive software environment based on our open-source toolkit for interactive medical image processing  ... 
doi:10.3348/kjr.2009.10.6.559 pmid:19885311 pmcid:PMC2770821 fatcat:6jezjc44afd7hcvjg62pibittm

New Techniques for Determining the Longitudinal Effects of Local Hemodynamics on the Intima-Media Thickness in Arteriovenous Fistulae in an Animal Model

Ehsan Rajabi-Jagahrgh, Prabir Roy-Chaudhury, Yang Wang, Marwan Al-Rjoub, Begona Campos-Naciff, Ann Choe, Charles Dumoulin, Rupak K. Banerjee
2013 Seminars in dialysis  
A radiopaque marker (ROM) was sutured to the AVF at the day of surgery, which was visible in the CT-scan images, micro-MRI, and histology sections.  ...  Immediately after sacrificing the pig, a procedure was developed to create a cast from the AVF and thus, maintaining the in vivo state of the AVF during the histology process.  ...  Acknowledgements This study was partially funded by a) Deans Collage of Engineering Research Fund, University of Cincinnati, and b) VA Merit G100850-7200600000-1-1006891. We acknowledge Dr.  ... 
doi:10.1111/sdi.12162 pmid:24261988 fatcat:g7drmsv4jneo3c3bqz3ewqcudy

Transfer Function design toolbox for full-color volume datasets

Martin Falk, Ingrid Hotz, Patric Ljung, Darren Treanor, Anders Ynnerman, Claes Lundstrom
2017 2017 IEEE Pacific Visualization Symposium (PacificVis)  
We propose a novel TF design toolbox based on color similarity which is used to adjust opacity as well as replacing colors.  ...  Thereby, colors representing a higher share of the dataset are depicted more prominently, thus providing a higher sensitivity for fine-tuning TF widgets.  ...  The image slides of the colorectal polyp were provided by Neil Shepherd of Gloucester Royal Infirmary, UK, and scanned by Leeds University hospital, UK.  ... 
doi:10.1109/pacificvis.2017.8031591 dblp:conf/apvis/FalkHLTYL17 fatcat:mduh6q5smrc2nov7o7lamzvuqa

Interactive Visualization of 3D Histopathology in Native Resolution

2018 IEEE Transactions on Visualization and Computer Graphics  
Despite this, our developed application supports interactive study of 3D histology datasets at native resolution.  ...  As we will show in the paper, studying volumetric histology data will open up novel and useful opportunities for both research and clinical practice.  ...  The liver cirrhosis data, the healthy liver data, and the mouse embryo data are courtesy of University of Leeds, UK. The image slides of the colorectal polyp were provided by Prof.  ... 
doi:10.1109/tvcg.2018.2864816 pmid:30130214 fatcat:tiup5byainbqda6oxmygg5srs4

An imaging workflow for characterizing phenotypical change in large histological mouse model datasets

Kishore Mosaliganti, Tony Pan, Randall Ridgway, Richard Sharp, Lee Cooper, Alex Gulacy, Ashish Sharma, Okan Irfanoglu, Raghu Machiraju, Tahsin Kurc, Alain de Bruin, Pamela Wenzel (+3 others)
2008 Journal of Biomedical Informatics  
Result: This workflow includes four major components: (i) serial section image acquisition, (ii) image preprocessing, (iii) image analysis involving 2D pair-wise registration, 2D segmentation and 3D reconstruction  ...  The specific application is a study of the morphological change in a mouse placenta induced by knocking out the retinoblastoma gene.  ...  Acknowledgments This work was supported in part by funding from the National Institutes of Health NIBIB BISTI P20-EB000591, and The National Science Foundation (Grants CNS-0615155 and CNS-0509326).  ... 
doi:10.1016/j.jbi.2008.03.013 pmid:18502696 pmcid:PMC2657595 fatcat:manfzwyk5vag3kjhy7ykpgntei

Image-based histologic grade estimation using stochastic geometry analysis

Sokol Petushi, Jasper Zhang, Aladin Milutinovic, David E. Breen, Fernando U. Garcia, Ronald M. Summers, Bram van Ginneken
2011 Medical Imaging 2011: Computer-Aided Diagnosis  
A second algorithm was developed to apply stochastic geometry and texture analysis measurements to the segmented images and to produce shape distributions, transforming the original color images into a  ...  We developed a customized hybrid semi-automated segmentation algorithm to cluster the raw image data and reduce the image domain complexity to a binary representation with the foreground representing regions  ...  William Regli for his helpful comments about the project. Support for this research was provided by the U.S. Army Medical Research Acquisition Activity; Cooperative Agreement W81XWH 04-1-0419.  ... 
doi:10.1117/12.876346 dblp:conf/micad/PetushiZMBG11 fatcat:p3zgzehx3fckhdmhfccgyr5gxm

Tumor Cell Load and Heterogeneity Estimation From Diffusion-Weighted MRI Calibrated With Histological Data: an Example From Lung Cancer

Yi Yin, Oliver Sedlaczek, Benedikt Muller, Arne Warth, Margarita Gonzalez-Vallinas, Bernd Lahrmann, Niels Grabe, Hans-Ulrich Kauczor, Kai Breuhahn, Irene E. Vignon-Clementel, Dirk Drasdo
2018 IEEE Transactions on Medical Imaging  
Color deconvolution followed by cell nuclei segmentation was performed on digitized histological images to determine local and cell-type specific 2d (two-dimensional) densities. From these the 3d  ...  Diffusion-weighted magnetic resonance imaging (DWI) is a key non-invasive imaging technique for cancer diagnosis and tumor treatment assessment, reflecting Brownian movement of water molecules in tissues  ...  ACKNOWLEDGMENT We thank Johannes Lotz and Janine Olesch for providing us with the registered images ( [38] ). We also thank the reviewers for their useful comments.  ... 
doi:10.1109/tmi.2017.2698525 pmid:28463188 fatcat:dspd2rifpvhlhgjsrpc6cuyxby

Advances in three-dimensional reconstruction of the experimental spinal cord injury

B.S. Duerstock, C.L. Bajaj, V. Pascucci, D. Schikore, K.N. Lin, R.B. Borgens
2000 Computerized Medical Imaging and Graphics  
We also show for the first time, that determination of the volume and surface area of pathological features is possible using the reconstructed 3D images themselves.  ...  His Center's research and the development of treatments for spinal injury have received national and international attention in both the printed media (Discover Magazine, The New Scientist, Time Magazine  ...  Acknowledgements We appreciate the technical aid of Debra Bohnert and Loren Moriarty during the conduct of these experiments and thank Carie Brackenbury and Jacqueline Libhart for aid in manuscript preparation  ... 
doi:10.1016/s0895-6111(00)00034-3 pmid:11008186 fatcat:txgxl2iddvb4xpotrp6szaaae4

Mapping of Metabolic Heterogeneity of Glioma Using MR-Spectroscopy

Pamela Franco, Irene Huebschle, Carl Philipp Simon-Gabriel, Karam Dacca, Oliver Schnell, Juergen Beck, Hansjoerg Mast, Horst Urbach, Urs Wuertemberger, Marco Prinz, Jonas A. Hosp, Daniel Delev (+2 others)
2021 Cancers  
Here, we report a prospective clinical imaging trial (DRKS00019855) which aimed to develop a novel MR-spectroscopy-based algorithm for in-depth characterization of brain lesions and prediction of molecular  ...  The importance of developing automated analysis tools for 1H-MRS lies in the possibility of a straightforward application and simplified interpretation of metabolic and genetic data that allow for incorporation  ...  Acknowledgments: Some images on Figure 1 and Figure S1 were created with BioRender.com. Conflicts of Interest: No potential conflicts of interest were disclosed by the authors.  ... 
doi:10.3390/cancers13102417 pmid:34067701 pmcid:PMC8155922 fatcat:3bqwladytncl3l2xgscgmnsh54

Plexus Convolutional Neural Network (PlexusNet): A novel neural network architecture for histologic image analysis [article]

Okyaz Eminaga, Mahmoud Abbas, Christian Kunder, Andreas M. Loening, Jeanne Shen, James D. Brooks, Curtis P. Langlotz, Daniel L. Rubin
2020 arXiv   pre-print
In conclusion, PlexusNet represents a novel model architecture for histological image analysis that achieves classification performance comparable to other models while providing orders-of-magnitude parameter  ...  We found that the partitioning of the development set influences the model calibration for all models.  ...  Our goal was to develop a novel CNN architecture that facilitated the training of a well-calibrated model tailored to the specific needs of histological discrimination of cancer from non-cancer, which  ... 
arXiv:1908.09067v2 fatcat:xhwadz5ywnaslmvbevsrn2n5gi

Systematic analysis of cell phenotypes and cellular social networks in tissues using the histology topography cytometry analysis toolbox (histoCAT) [article]

Denis Schapiro, Hartland Warren Jackson, Swetha Raghuraman, Vito Riccardo Tomaso Zanotelli, Jana R Fischer, Daniel Schulz, Charlotte Giesen, Raul Catena, Zsuzsanna Varga, Bernd Bodenmiller
2017 bioRxiv   pre-print
We have developed a computational histology topography cytometry analysis toolbox (histoCAT) to enable the interactive, quantitative, and comprehensive exploration of phenotypes of individual cells, cell-to-cell  ...  We highlight the unique abilities of histoCAT by analysis of highly multiplexed mass cytometry images of human breast cancer tissues.  ...  ACKNOWLEDGEMENTS We would like to thank the Bodenmiller lab for support and fruitful discussions.  ... 
doi:10.1101/109207 fatcat:ahr6zg7jkzagjaxji3qfjz4cqu

Convolutional Neural Networks for cytoarchitectonic brain mapping at large scale

Christian Schiffer, Hannah Spitzer, Kai Kiwitz, Nina Unger, Konrad Wagstyl, Alan C. Evans, Stefan Harmeling, Katrin Amunts, Timo Dickscheid
2021 NeuroImage  
Here we present a new workflow for mapping cytoarchitectonic areas in large series of cell-body stained histological sections of human postmortem brains.  ...  It is based on a Deep Convolutional Neural Network (CNN), which is trained on a pair of section images with annotations, with a large number of un-annotated sections in between.  ...  Conclusion A novel method based on Convolutional Neural Networks (CNNss) was introduced for automated mapping of cytoarchitectonic areas in large series of histological human brain sections.  ... 
doi:10.1016/j.neuroimage.2021.118327 pmid:34224853 fatcat:hyfbr56g3rfttlukoe7dpnx6e4
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