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A flexible and robust approach for segmenting cell nuclei from 2D microscopy images using supervised learning and template matching

Cheng Chen, Wei Wang, John A. Ozolek, Gustavo Rohde
2018
We describe a new supervised learning-based template matching approach for segmenting cell nuclei from microscopy images.  ...  The method uses examples selected by a user for building a statistical model that captures the texture and shape variations of the nuclear structures from a given dataset to be segmented.  ...  We note that template matching-based methods for image segmentation have long been used for segmenting biomedical images.  ... 
doi:10.1184/r1/6096191.v1 fatcat:jvamathwpbanlblyxl2togprdq

Automated characterization of bacteria in confocal microscope images

Felida Roa, Antonio Bravo, Alexis Valery
2008 2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops  
a template matching procedure.  ...  The problem of bacteria characterization from images acquired in microscopy is considered.  ...  Udupa, from University of Pennsylvania, for the fruitful discussions about segmentation methods sustained during the IEEE EMBS 2006 International Summer School on Biomedical Imaging in Berder Island, France  ... 
doi:10.1109/cvprw.2008.4563026 dblp:conf/cvpr/RoaBV08 fatcat:twr2afyavzb5fh3karbjikptum

Efficient Extraction of Macromolecular Complexes from Electron Tomograms Based on Reduced Representation Templates [chapter]

Xiao-Ping Xu, Christopher Page, Niels Volkmann
2015 Lecture Notes in Computer Science  
Standard template matching approaches tend to generate large amounts of false positives.  ...  Using this approach we see a reduction of about 50% false positives with matched-filter approaches to below 5%.  ...  Reduced representation used for template matching in B.  ... 
doi:10.1007/978-3-319-23192-1_35 pmid:30058003 pmcid:PMC6063751 fatcat:2vafq53uo5e3ro7jnaxqf2p4yq

Multi-template matching: a versatile tool for object-localization in microscopy images

Laurent S. V. Thomas, Jochen Gehrig
2020 BMC Bioinformatics  
Therefore, we propose a new straightforward and generic approach for object-localization by template matching that utilizes multiple template images to improve the detection capacity.  ...  To provide an easy-to-use method for the automatic localization of objects of interest in microscopy images, we implemented multi-template matching as a Fiji plugin, a KNIME workflow and a python package  ...  Competing interests Both authors are employees of ACQUIFER, a division of DITABIS Digital Biomedical Imaging Systems AG.  ... 
doi:10.1186/s12859-020-3363-7 pmid:32024462 pmcid:PMC7003318 fatcat:s5unl6er4zf6noykpbzrqwbfaq

SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects

Michael Kloster, Gerhard Kauer, Bánk Beszteri
2014 BMC Bioinformatics  
Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification  ...  While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into  ...  images used.  ... 
doi:10.1186/1471-2105-15-218 pmid:24964954 pmcid:PMC4087246 fatcat:xtgztmzse5cw7mkwxfj5zxq5c4

In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology

Shoh Asano, Benjamin D. Engel, Wolfgang Baumeister
2016 Journal of Molecular Biology  
Unlike many other imaging approaches, cryo-ET provides a label-free method of detecting biological structures, relying on the intrinsic contrast of frozen cellular material for direct identification of  ...  Here, we review these technical developments and outline a detailed computational workflow for in situ structural analysis.  ...  Journal of microscopy 172, 55-61. 33. Studer, D., Graber W., Al-Amoudi A. & Eggli P. (2001). A new approach for cryofixation by highpressure freezing. Journal of microscopy 203, 285-94. 34.  ... 
doi:10.1016/j.jmb.2015.09.030 pmid:26456135 fatcat:ristqzkblreuhny7ohqecagqxi

Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections

Chen Yang, Daniel Niedieker, Frederik Großerüschkamp, Melanie Horn, Andrea Tannapfel, Angela Kallenbach-Thieltges, Klaus Gerwert, Axel Mosig
2015 BMC Bioinformatics  
In recent years, hyperspectral microscopy techniques such as infrared or Raman microscopy have been applied successfully for diagnostic purposes.  ...  Results: We propose a corresponding registration algorithm that addresses this registration problem, and demonstrate the robustness of our approach in different constellations of microscopes.  ...  Whenever dealing with a template matching scenario, the stained images were segmented into ten clusters, while the smaller spectral image was segmented into eight clusters.  ... 
doi:10.1186/s12859-015-0804-9 pmid:26607812 pmcid:PMC4659215 fatcat:nzebg7sjnzh7rcr3xtnyiwvblm

Large volume reconstruction from laser scanning microscopy using micro-CT as a template for deformation compensation

A. Subramanian, A. Krol, A. H. Poddar, R. L. Price, R. Swarnkar, D. H. Feiglin, Josien P. W. Pluim, Joseph M. Reinhardt
2007 Medical Imaging 2007: Image Processing  
template in the volume reconstruction from a very large number of LSM images.  ...  to correct for non-uniform illumination and noise; (iii) Volume matching of a synthesized physical section to a corresponding sub-volume of µCT; (iv) Affine registration of the physical section to the  ...  Here, we investigate utilization of micro-CT as a template for the deformation correction. We had previously reported application of this approach to the volume synthesis [3] .  ... 
doi:10.1117/12.709855 dblp:conf/miip/SubramanianKPPS07 fatcat:merm3oskprelhge2v4oyxpg4p4

Mapping organism expression levels at cellular resolution in developing Drosophila

David W. Knowles, Soile Keranen, Mark D. Biggin, Damir Sudar, Jose-Angel Conchello, Carol J. Cogswell, Tony Wilson
2002 Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing IX  
Embryos at different stages of development are labeled for total DNA and specific gene products using different fluorophors and imaged in 3D with confocal microscopy.  ...  Innovative steps have been made which allow the DNA-image to be automatically segmented to produce a morphological mask of the individual nuclear boundaries.  ...  The images are automatically segmented by an algorithm using a combination of local brightness thresholding and template matching to locate the nuclei.  ... 
doi:10.1117/12.467832 fatcat:22gvhrhukjek5defjn5bxwpo4u

Assembling models of embryo development: Image analysis and the construction of digital atlases

Carlos Castro-González, María J. Ledesma-Carbayo, Nadine Peyriéras, Andrés Santos
2012 Birth Defects Research Part C Embryo Today Reviews  
2D gene expressions. b No matching procedure: Each specimen was directly employed as the template of its corresponding developmental stage. c 3D+t live imaging.  ...  The latter as well as data integration in a prototypic model, rely on image processing strategies.  ...  MATCHING PROCEDURES A matching procedure is required to import each specimen (the source) into the template according to the maximization of a likelihood criteria.  ... 
doi:10.1002/bdrc.21012 pmid:22692885 fatcat:cqoiiquq6jegpilb7blhwqkmuq

A Statistical Dictionary Approach to Automated Orientation Determination from Precession Electron Diffraction Patterns

A. Wang, A.C. Leff, M.L. Taheri, M. De Graef
2015 Microscopy and Microanalysis  
The crystal orientation for a given PED pattern is then obtained by finding the best match against the dictionary.  ...  as a dictionary-based approach.  ...  The crystal orientation for a given PED pattern is then obtained by finding the best match against the dictionary. Rauch et al.  ... 
doi:10.1017/s1431927615007023 fatcat:kya2wcz3izfubbpxyicma6ghvq

Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions

Niels Volkmann
2012 Current Opinion in Cell Biology  
While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured  ...  to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale.  ...  Dorit Hanein for critically reading the manuscript and for providing valuable input. I thank Dr. Roman Koning for kindly providing the tomogram used in Figure 1 .  ... 
doi:10.1016/j.ceb.2011.11.002 pmid:22152946 pmcid:PMC3294126 fatcat:3wrtq2ez3bgqjcwyzr3f77z554

A framework for feedback-based segmentation of 3D image stacks

Johannes Stegmaier, Nico Peter, Julia Portl, Ira V. Mang, Rasmus Schröder, Heike Leitte, Ralf Mikut, Markus Reischl
2016 Current Directions in Biomedical Engineering  
Therefore, we present a workflow for 3D segmentation being able to forecast segments based on a user-given ground truth.  ...  However, automatic segmentation does not deliver high accuracy in optically dense images and manual segmentation lowers the throughput drastically.  ...  Both template matching approaches (NCC and CorrCoeff) failed to predict the first slice and are thus not practically usable in this scenario.  ... 
doi:10.1515/cdbme-2016-0097 fatcat:ses6eumdtvhntb52o4xinhtd7y

Automatic detection of endothelial cells in 3D angiogenic sprouts from experimental phase contrast images

MengMeng Wang, Lee-Ling Sharon Ong, Justin Dauwels, H. Harry Asada, Sébastien Ourselin, Martin A. Styner
2015 Medical Imaging 2015: Image Processing  
Two template matching based approaches are proposed to automatically detect the unlabeled ECs in the angiogenic sprouts from the acquired experimental phase contrast images.  ...  More accurate numerical results are obtained for approach I (PLSR) compared to approach II (PCA & SVM) for cell detection.  ...  ACKNOWLEDGMENTS This research was supported by the National Research Foundation Singapore through the Singapore MIT Alliance for Research and Technologys BioSystems and Micromechanics Inter-Disciplinary  ... 
doi:10.1117/12.2081819 dblp:conf/miip/WangODA15 fatcat:ojjjprjpmjbpdnjf4j355235ye

Parameter-Free Binarization and Skeletonization of Fiber Networks from Confocal Image Stacks

Patrick Krauss, Claus Metzner, Janina Lange, Nadine Lang, Ben Fabry, Francisco José Esteban
2012 PLoS ONE  
The method is based on a template matching algorithm that simultaneously performs a binarization and skeletonization of the network.  ...  Furthermore, the template matching threshold is iteratively optimized to ensure that the final skeletonized network obeys a universal property of voxelized random line networks, namely, solid-phase voxels  ...  However, the situation is much simpler when only 2D crosssections are used for the template matching: The vertical crosssection of a broadened line segment with a plane is a elliptical spot of finite size  ... 
doi:10.1371/journal.pone.0036575 pmid:22606273 pmcid:PMC3351466 fatcat:6pc52cz7cfbxjcq23srr4eqvl4
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