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Hybrid Segmentation Framework for Tissue Images Containing Gene Expression Data [chapter]

Musodiq Bello, Tao Ju, Joe Warren, James Carson, Wah Chiu, Christina Thaller, Gregor Eichele, Ioannis A. Kakadiaris
2005 Lecture Notes in Computer Science  
The subdivision mesh provides a common coordinate system for internal brain data through which gene expression patterns can be compared across images.  ...  In this work, we propose a new automatic method that results in the segmentation of gene expression images into distinct anatomical regions in which the expression can be quanti ed and compared with other  ...  Fig. 5 . 5 Comparison of the accuracy of t of four major anatomical regions in 64 expression images. Fig. 6 . 6 Mean of the accuracy of t in 64 images using the hybrid segmentation framework.  ... 
doi:10.1007/11566465_32 fatcat:butn5xngx5fgldt6fh5e46gyom

Learning-Based Segmentation Framework for Tissue Images Containing Gene Expression Data

M. Bello, Tao Ju, J. Carson, J. Warren, Wah Chiu, I.A. Kakadiaris
2007 IEEE Transactions on Medical Imaging  
This atlas, which provides a common coordinate system for internal brain data, is being used to create a searchable database of gene expression patterns in the adult mouse brain.  ...  Our framework annotates the images about four times faster and has achieved a median spatial overlap of up to 0.92 compared with expert segmentation in 64 images tested.  ...  Eichele for their help with data acquisition and annotation.  ... 
doi:10.1109/tmi.2007.895462 pmid:17518066 fatcat:nl2ag54llfei7bfjncmifr5ebi

dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues

Kristen R Maynard, Madhavi Tippani, Yoichiro Takahashi, BaDoi N Phan, Thomas M Hyde, Andrew E Jaffe, Keri Martinowich
2020 Nucleic Acids Research  
We present a framework for generating and analyzing smFISH data in complex tissues while overcoming autofluorescence and increasing multiplexing capacity.  ...  In summary, we provide experimental workflows, imaging acquisition and analytic strategies for quantification and biological interpretation of smFISH data in complex tissues.  ...  and curation of brain tissue donations for this study.  ... 
doi:10.1093/nar/gkaa312 pmid:32383753 pmcid:PMC7293004 fatcat:sm7l6czuqvdndkot6eulvu7iba

dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues [article]

Kristen R Maynard, Madhavi Tippani, Yoichiro Takahashi, BaDoi N Phan, Thomas M Hyde, Andrew E Jaffe, Keri Martinowich
2019 bioRxiv   pre-print
We present a framework for generating and analyzing smFISH data in complex tissues while overcoming autofluorescence and increasing multiplexing capacity.  ...  In summary, we provide experimental workflows, imaging acquisition and analytic strategies for quantification and biological interpretation of smFISH data in complex tissues.  ...  We thank Ed Lein and Jennie Close at the Allen Brain Institute for generously sharing RNAscope image data. We thank Daniel Weinberger and Stephanie Page for comments on the manuscript.  ... 
doi:10.1101/781559 fatcat:yjrocjbq3zfpldlvq4kpkdfe54

Landmark-Driven, Atlas-Based Segmentation of Mouse Brain Tissue Images Containing Gene Expression Data [chapter]

Ioannis A. Kakadiaris, Musodiq Bello, Shiva Arunachalam, Wei Kang, Tao Ju, Joe Warren, James Carson, Wah Chiu, Christina Thaller, Gregor Eichele
2004 Lecture Notes in Computer Science  
To perform such an association for a large amount of data, reliable automated methods that characterize the distribution of gene expression in relation to a standard anatomical model are required.  ...  The resulting large-scale annotation will help scientists interpret gene expression patterns more rapidly and accurately.  ...  Methods Experimental Data In situ hybridization to label cells expressing a gene of interest was performed on 20µmthick serially sliced cross-sections of the postnatal day 7 (P7) C57BL/6 mouse brain,  ... 
doi:10.1007/978-3-540-30135-6_24 fatcat:yib4cg2af5er3lohmyelb4akzu

Cell segmentation-free inference of cell types from in situ transcriptomics data

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle (+2 others)
2021 Nature Communications  
Here, we present a method called Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation (SSAM), a robust cell segmentation-free computational framework for identifying cell-types  ...  However, inaccurate cell segmentation reduces the efficacy of cell-type identification and tissue characterization.  ...  The Github repository also contains the extensive diagnostic plots used for parameter selection, and choice of removal or merging of clusters.  ... 
doi:10.1038/s41467-021-23807-4 pmid:34112806 fatcat:dx65syjkxbbxno3libawc345ma

Segmentation-free inference of cell-types from in situ transcriptomics data [article]

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Simone Codeluppi, Matthias Schlesner, Bosiljka Tasic, Roland Eils, Naveed Ishaque
2019 bioRxiv   pre-print
SSAM outperforms segmentation-based results, demonstrating that segmentation of cells is not required for inferring cell-type signatures, cell-type organization or tissue domains.  ...  We apply SSAM to three mouse brain tissue images: the somatosensory cortex imaged by osmFISH, the hypothalamic preoptic region by MERFISH, and the visual cortex by multiplexed smFISH.  ...  on data analysis.  ... 
doi:10.1101/800748 fatcat:h3hquog3gjgefdrn7ycfwa543u

Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals

Christopher P. Arnold, Analí Migueles Lozano, Frederick G. Mann, Stephanie H. Nowotarski, Julianna O. Haug, Jeffrey J. Lange, Chris W. Seidel, Alejandro Sánchez Alvarado
2021 Nature Communications  
Collectively, our study establishes adult stage roles for Hox genes in the regulation of tissue segmentation and behavior associated with asexual reproduction.  ...  We report functions for Hox genes in A/P tissue segmentation and transverse fission behavior underlying asexual reproduction in adult planarian flatworms, Schmidtea mediterranea.  ...  Acknowledgements We thank members of the ASA laboratory for discussion and advice and Robb Krumlauf for their comments.  ... 
doi:10.1038/s41467-021-26986-2 pmid:34795249 pmcid:PMC8602322 fatcat:ri3au42vxfhb5mzcgqc64sowle

Parallelized analysis of spatial gene expression patterns by database integration [article]

Daisuke Miyamoto, Hidetoshi Ikeno, Yuko Okamura-Oho, Akira Sato, Teiichi Furuichi, Yoshihiro Okumura, Yoko Yamaguchi, Ryohei Kanzaki
2018 bioRxiv   pre-print
We first transformed ISH images of 10 regionally expressed genes and compared them to signals of corresponding 3D expression images in ViBrism DB for evaluating the integration schema: two types of data  ...  We applied the framework to 2,810 para-sagittal sectioned mouse brain 2D images of in situ hybridization (ISH), archived in the BrainTx database (http://www.cdtdb.neuroinf.jp).  ...  Parallel processing of registration for massive image data Our framework was parallelized within a PC cluster; this acceleration provided a new scheme for large-scale analysis of gene expression.  ... 
doi:10.1101/386086 fatcat:ozcr2vbcrzerzmolhpgeekgkt4

Fundamentals of cDNA microarray data analysis

Yuk Fai Leung, Duccio Cavalieri
2003 Trends in Genetics  
We thank Alice Yu Ming Lee and Abel Chiu Shun Chun for their critical comments on this manuscript.  ...  A better framework of significance inference includes calculation of a statistic based on replicate array data for ranking genes according to their possibilities of differential expression and selection  ...  Biological replication is particularly important for expression profiling of disease tissues, because there might be variability of expression among the same tissue type or tissue heterogeneity.  ... 
doi:10.1016/j.tig.2003.09.015 pmid:14585617 fatcat:coiymseew5cxbpaykzu2632jyi

Gene expression reliability estimation through cluster-based analysis

Luca Sterpone, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano
2009 2009 IEEE International Workshop on Medical Measurements and Applications  
The measurement of gene expressions is performed on images generated by optical inspection of microarray devices which allow the simultaneous analysis of thousands of genes.  ...  The images produced by these devices are used to calculate the expression levels of mRNA in order to draw diagnostic information related to human disease.  ...  By examining the expression of several genes simultaneously, it is possible to identify and study the gene expression patterns of a type of cellular's tissue under a certain physiological condition [1  ... 
doi:10.1109/memea.2009.5167990 fatcat:rxomirihqfgobmhwjzyjmnopb4

Automated pipeline for atlas-based annotation of gene expression patterns: Application to postnatal day 7 mouse brain

James Carson, Tao Ju, Musodiq Bello, Christina Thaller, Joe Warren, Ioannis A. Kakadiaris, Wah Chiu, Gregor Eichele
2010 Methods  
Massive amounts of image data have been collected and continue to be generated for representing cellular gene expression throughout the mouse brain.  ...  The steps include imaging tissue slices, detecting cellular gene expression levels, spatial registration with an atlas, and textual annotation.  ...  Keck Foundation to the Gulf Coast Consortia through the Keck Center for Computational and Structural Biology.  ... 
doi:10.1016/j.ymeth.2009.08.005 pmid:19698790 pmcid:PMC2818703 fatcat:qt4slmfv2vh3paia7enqlcmrcm

Image analysis for understanding embryo development: a bridge from microscopy to biological insights

MA Luengo-Oroz, MJ Ledesma-Carbayo, N Peyriéras, A Santos
2011 Current Opinion in Genetics and Development  
validation methodologies for cell membrane shape identification, single cell gene expression quantification from in situ hybridization data, and multidimensional image registration algorithms for the construction  ...  the potential of imaging data for biological insights.  ...  that integrate both cell lineage and gene expression data.  ... 
doi:10.1016/j.gde.2011.08.001 pmid:21893410 fatcat:woaff5emnje4rg64otdqzx6yry

Regeneration in the Segmented Annelid Capitella teleta

Elaine C. Seaver, Danielle M. de Jong
2021 Genes  
Annelids have long been models for regeneration studies due to their impressive regenerative abilities.  ...  Furthermore, the group exhibits variation in adult regeneration abilities with some species able to replace anterior segments, posterior segments, both or neither.  ...  Acknowledgments: We thank Lauren Kunselman and Alicia Boyd for comments on the manuscript and Trey de Leon for cloning the myc gene.  ... 
doi:10.3390/genes12111769 pmid:34828375 pmcid:PMC8623021 fatcat:r3ccurq32jbgjmdwvmgqhzytf4

A deep learning based method for large-scale classification, registration, and clustering of in-situ hybridization experiments in the mouse olfactory bulb

Alexander Andonian, Daniel Paseltiner, Travis J. Gould, Jason B. Castro
2019 Journal of Neuroscience Methods  
The Allen Mouse Brain Atlas allows study of the brain's molecular anatomy at cellular scale, for thousands genes.  ...  To fully leverage this resource, one must register histological images of brain tissue - a task made challenging by the brain's structural complexity and heterogeneity, as well as inter-experiment variability  ...  Acknowledgements We thank the Allen Institute for making these data available. JBC is supported by an NSF CAREER award (1553279).  ... 
doi:10.1016/j.jneumeth.2018.12.003 pmid:30529409 pmcid:PMC6637410 fatcat:4g63heh6czg3jllwflkaxfn47i
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