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Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets

Richard J Giuly, Maryann E Martone, Mark H Ellisman
2012 BMC Bioinformatics  
Overall, our results show that use of contour pair classification and level set operations improve segmentation accuracy beyond patch classification alone.  ...  The method consists of three steps. The first is a random forest patch classification step operating directly on 2D image patches. The second step consists of contour-pair classification.  ...  Authors' contributions RJG designed the segmentation pipeline presented here, implemented the code, tested it against human segmentation, and drafted the manuscript.  ... 
doi:10.1186/1471-2105-13-29 pmid:22321695 pmcid:PMC3293777 fatcat:udd5fprx7jhala2adez54rr7c4

A workflow for the automatic segmentation of organelles in electron microscopy image stacks

Alex J. Perez, Mojtaba Seyedhosseini, Thomas J. Deerinck, Eric A. Bushong, Satchidananda Panda, Tolga Tasdizen, Mark H. Ellisman
2014 Frontiers in Neuroanatomy  
Here, we present a novel method for the automatic segmentation of organelles in 3D EM image stacks.  ...  data sets that can include hundreds to thousands of whole cells.  ...  AUTHORS AND CONTRIBUTORS  ... 
doi:10.3389/fnana.2014.00126 pmid:25426032 pmcid:PMC4224098 fatcat:3swx32i6w5hyliy2kmvlegtmfm

Video Bioinformatics Methods for Analyzing Cell Dynamics: A Survey [chapter]

Nirmalya Ghosh
2015 Computational Biology  
segmentation to cellular feature extraction and selection, classification into different phenotypes, and exploration of hidden content-based patterns in bioimaging databases.  ...  Understanding cellular and subcellular interrelations, spatiotemporal dynamic activities, and complex biological processes from quantitative microscopic video is an emerging field of research.  ...  maximization of a Kolmogorov complexity measure, then active contours are initialized and expanded for level set segmentation [80] .  ... 
doi:10.1007/978-3-319-23724-4_2 fatcat:wjsaagwnpbgmziy662tsmw6hv4

A modular hierarchical approach to 3D electron microscopy image segmentation

Ting Liu, Cory Jones, Mojtaba Seyedhosseini, Tolga Tasdizen
2014 Journal of Neuroscience Methods  
Also, we develop a semi-automatic method that utilizes the intermediate outputs of our automatic algorithm and achieves intra-segmentation with minimal user intervention.  ...  The experimental results show that our automatic method can achieve close-to-human intra-segmentation accuracy and state-of-the-art inter-section reconstruction accuracy.  ...  the University of California, San Diego for providing the mouse neuropil data set, the Jeff Lichtman Lab at Harvard University for providing the mouse cortex data set, and Alessandro Guisti and Dan Ciresan  ... 
doi:10.1016/j.jneumeth.2014.01.022 pmid:24491638 pmcid:PMC3970427 fatcat:3bm4j244infyzjgs4xjqlcv2um

Automatic Reconstruction of Mitochondria and Endoplasmic Reticulum in Electron Microscopy Volumes by Deep Learning

Jing Liu, Linlin Li, Yang Yang, Bei Hong, Xi Chen, Qiwei Xie, Hua Han
2020 Frontiers in Neuroscience  
However, manual segmentation of mitochondria and ER from EM images is time consuming and thus unable to meet the demands of large data analysis.  ...  We propose a novel recurrent neural network to detect and segment mitochondria and a fully residual convolutional network to reconstruct the ER.  ...  Recently, variety of methods have been developed to automatically detect and segment mitochondria (Liu et al., 2018; Xiao et al., 2018; Xie et al., 2018b) .  ... 
doi:10.3389/fnins.2020.00599 pmid:32792893 pmcid:PMC7394701 fatcat:lfk7yzssird4dpv4usfuwkgqeu

DeepACSON automated segmentation of white matter in 3D electron microscopy

Ali Abdollahzadeh, Ilya Belevich, Eija Jokitalo, Alejandra Sierra, Jussi Tohka
2021 Communications Biology  
mitochondria with excellent evaluation scores.  ...  We applied DeepACSON to ten EM volumes of rats after sham-operation or traumatic brain injury, segmenting hundreds of thousands of long-span myelinated axons, thousands of cell nuclei, and millions of  ...  Acknowledgements This work was supported by the Academy of Finland (grant #316258 to J.T. and grant #323385 to A.S.) and Biocenter Finland and the University of Helsinki (I.B., E.J., and SBEM imaging).  ... 
doi:10.1038/s42003-021-01699-w pmid:33568775 fatcat:n7omwahme5c3rbqefozqdvfuru

Citizen science, cells and CNNs - deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations [article]

Helen Spiers, Harry Songhurst, Luke Nightingale, Joost de Folter, Roger Hutchings, Christopher J Peddie, Anne Weston, Amy Strange, Steve Hindmarsh, Chris Lintott, Lucy M Collinson, Martin L Jones
2020 bioRxiv   pre-print
a highly accurate machine learning algorithm for automatic segmentation of the nuclear envelope, which we share here, in addition to our archived benchmark data.  ...  We present our approach for aggregating multiple volunteer annotations to generate a high quality consensus segmentation, and demonstrate that data produced exclusively by volunteers can be used to train  ...  A benchmark serial image data set was gener-and Methods).  ... 
doi:10.1101/2020.07.28.223024 fatcat:3k5gmdi4fnautovj4b3kcmvbgq

Functional connectomics spanning multiple areas of mouse visual cortex [article]

MICrONS Consortium, J. Alexander Bae, Mahaly Baptiste, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Brendan Celii, Erick Cobos, Forrest Collman, Nuno Maçarico da Costa (+64 others)
2021 bioRxiv   pre-print
The functional data were co-registered with electron microscopy (EM) data of the same volume which were automatically segmented, reconstructing more than 200,000 cells (neuronal and non-neuronal) and 524  ...  Here we release this dataset as an open access resource to the scientific community including a set of analysis tools that allows easy data access, both programmatically and through a web user interface  ...  , of IARPA, DoI/IBC, or the U.S.  ... 
doi:10.1101/2021.07.28.454025 fatcat:z45ycgt5jjba7jplliapixrz4q

Synaptic Specializations of Melanopsin-Retinal Ganglion Cells in Multiple Brain Regions Revealed by Genetic Label for Light and Electron Microscopy

Keun-Young Kim, Luis C. Rios, Hiep Le, Alex J. Perez, Sébastien Phan, Eric A. Bushong, Thomas J. Deerinck, Yu Hsin Liu, Maya A. Ellisman, Varda Lev-Ram, Suyeon Ju, Sneha A. Panda (+6 others)
2019 Cell Reports  
version of a genetic probe for correlated light and electron microscopy (CLEM). ipRGCs project to multiple brain regions, and because the method labels the entire neuron, it was possible to analyze nerve  ...  The methods developed to enable this analysis should propel other CLEM studies of long-distance brain circuits at high resolution.  ...  David O'Keefe for help with preparing the manuscript and Daniela Boassa, Hiroyuki Hakozaki, Willy Wong, and Andrea Thor for technical support.  ... 
doi:10.1016/j.celrep.2019.09.006 pmid:31618632 pmcid:PMC7045601 fatcat:xvrskbagbvf6horpfcaep33zae

Whole-body integration of gene expression and single-cell morphology [article]

Hernando M. Vergara, Constantin Pape, Kimberly I. Meechan, Valentyna Zinchenko, Christel Genoud, Adrian A. Wanner, Benjamin Titze, Rachel M. Templin, Paola Y. Bertucci, Oleg Simakov, Pedro Machado, Emily L. Savage (+5 others)
2020 bioRxiv   pre-print
For this, we registered a whole-body cellular expression atlas to a high-resolution electron microscopy dataset, automatically segmented all cell somata and nuclei, and clustered the cells according to  ...  SummaryAnimal bodies are composed of hundreds of cell types that differ in location, morphology, cytoarchitecture, and physiology.  ...  Here, we found a 99.0% agreement with the automatic nuclear segmentation and a 90.3% agreement with the cellular segmentation (see Methods and Supplementary Figure 2A) .  ... 
doi:10.1101/2020.02.26.961037 fatcat:b4lzvy6ovfd65li6qq5ikoypxi

Modeling & Analysis

2003 NeuroImage  
All scans were semi-automatically segmented using in-house software.  ...  of lactate, consumption of pyruvate by mitochondria, and lactate exchanges through cell membranes.  ...  Images were normalized and segmented into gray and white matter and CSF [4].  ... 
doi:10.1016/s1053-8119(05)70006-9 fatcat:zff2suxcofbxvetfrwfwcxi3zm

The visualization of hepatic vasculature by X-ray micro-computed tomography

S. Ananda
2006 Journal of Electron Microscopy  
Yamamoto and Y. Ikuhara for useful discussions. This work was supported by the Kazato Research Foundation of Japan and JSPS KAKENHI Grant Numbers 17K14119 and 19H02606.  ...  Part of this work was supported by the Research & Development Initiative for Scientific Innovation of New Generation Batteries 2 (RISING 2) project from the New Energy and Industrial Technology Development  ...  Our proposed method accurately detected mitochondria, amyloplasts, chloroplasts, etioplasts, and Golgi stacks, indicating its broad utility to detect biological structures in TEM images.  ... 
doi:10.1093/jmicro/dfl015 pmid:16775217 fatcat:4udqurxlh5hjfjmq5nv6w2eroa

Wet Poster Session

2019 Biomedical Engineering  
Digital light microscopy techniques are among the most widely used methods in cell biology and medical research.  ...  Despite that, automated classification of objects such as cells or specific parts of tissues is difficult.  ...  We evaluated the effect of pneumatic muscle length on contractile force and length, and used the results to produce a functioning motor demonstrator.  ... 
doi:10.1515/bmt-2019-6023 fatcat:mxp5r64yufccjg7dwe4orqjssa

A connectome and analysis of the adult Drosophila central brain

Louis K Scheffer, C Shan Xu, Michal Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J Hayworth, Gary B Huang, Kazunori Shinomiya, Jeremy Maitlin-Shepard, Stuart Berg, Jody Clements, Philip M Hubbard (+96 others)
2020 eLife  
Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets.  ...  We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster.  ...  ), without being given any explicit pairings 1697 between elements of both sets.  ... 
doi:10.7554/elife.57443 pmid:32880371 pmcid:PMC7546738 fatcat:zv5uachzanatdmypjbq4c6zja4

A Connectome and Analysis of the Adult Drosophila Central Brain [article]

Louis K Scheffer, C Shan Xu, Michal Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J Hayworth, Gary Huang, Kazunori Shinomiya, Jeremy Maitlin-Shepard, Stuart Berg, Jody Clements, Philip M Hubbard (+93 others)
2020 biorxiv/medrxiv   pre-print
Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets.  ...  We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster.  ...  of fruitless expressing neurons, and Aljosha Nern, Michael B.  ... 
doi:10.1101/2020.04.07.030213 fatcat:6ixeg6juv5aazlhbxv5qs3t2am
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