[HTML][HTML] SYNAPSE: An international roadmap to large brain imaging

APJ Stampfl, Z Liu, J Hu, K Sawada, H Takano… - Physics Reports, 2023 - Elsevier
Since 2020, synchrotron radiation facilities in several Asia-Pacific countries have been
collaborating in a major project called “SYNAPSE”(Synchrotrons for Neuroscience: an Asia …

Transgenic Xenopus laevis for live imaging in cell and developmental biology

C Takagi, K Sakamaki, H Morita, Y Hara… - Development …, 2013 - Wiley Online Library
The stable transgenesis of genes encoding functional or spatially localized proteins, fused to
fluorescent proteins such as green fluorescent protein (GFP) or red fluorescent protein …

3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis

Y Tokuoka, TG Yamada, D Mashiko, Z Ikeda… - NPJ systems biology …, 2020 - nature.com
During embryogenesis, cells repeatedly divide and dynamically change their positions in
three-dimensional (3D) space. A robust and accurate algorithm to acquire the 3D positions …

Current automated 3D cell detection methods are not a suitable replacement for manual stereologic cell counting

C Schmitz, BS Eastwood, SJ Tappan… - Frontiers in …, 2014 - frontiersin.org
Stereologic cell counting has had a major impact on the field of neuroscience. A major
bottleneck in stereologic cell counting is that the user must manually decide whether or not …

A guided tour of selected image processing and analysis methods for fluorescence and electron microscopy

C Kervrann, CÓS Sorzano, ST Acton… - IEEE Journal of …, 2015 - ieeexplore.ieee.org
Microscopy imaging, including fluorescence micro scopy and electron microscopy, has
taken a prominent role in life science research and medicine due to its ability to investigate …

Accurate automatic detection of densely distributed cell nuclei in 3D space

Y Toyoshima, T Tokunaga, O Hirose… - PLoS computational …, 2016 - journals.plos.org
To measure the activity of neurons using whole-brain activity imaging, precise detection of
each neuron or its nucleus is required. In the head region of the nematode C. elegans, the …

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

Y Tohsato, KHL Ho, K Kyoda, S Onami - Bioinformatics, 2016 - academic.oup.com
Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have
produced a large amount of quantitative data on spatiotemporal dynamics of biological …

NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model

T Quan, T Zheng, Z Yang, W Ding, S Li, J Li, H Zhou… - Scientific reports, 2013 - nature.com
Drawing the map of neuronal circuits at microscopic resolution is important to explain how
brain works. Recent progresses in fluorescence labeling and imaging techniques have …

3d centroidnet: nuclei centroid detection with vector flow voting

L Wu, A Chen, P Salama, KW Dunn… - 2022 IEEE International …, 2022 - ieeexplore.ieee.org
Automated microscope systems are increasingly used to collect large-scale 3D image
volumes of biological tissues. Since cell boundaries are seldom delineated in these images …

iCut: an integrative cut algorithm enables accurate segmentation of touching cells

Y He, H Gong, B Xiong, X Xu, A Li, T Jiang, Q Sun… - Scientific reports, 2015 - nature.com
Individual cells play essential roles in the biological processes of the brain. The number of
neurons changes during both normal development and disease progression. High …