Whole-cell organelle segmentation in volume electron microscopy

L Heinrich, D Bennett, D Ackerman, W Park, J Bogovic… - Nature, 2021‏ - nature.com
Cells contain hundreds of organelles and macromolecular assemblies. Obtaining a
complete understanding of their intricate organization requires the nanometre-level, three …

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

AJ Perez, M Seyedhosseini, TJ Deerinck… - Frontiers in …, 2014‏ - frontiersin.org
Electron microscopy (EM) facilitates analysis of the form, distribution, and functional status of
key organelle systems in various pathological processes, including those associated with …

Progress towards mammalian whole-brain cellular connectomics

S Mikula - Frontiers in neuroanatomy, 2016‏ - frontiersin.org
Neurons are the fundamental structural units of the nervous system—ie, the Neuron Doctrine—
as the pioneering work of Santiago Ramón y Cajal in the 1880's clearly demonstrated …

Automatic whole cell organelle segmentation in volumetric electron microscopy

L Heinrich, D Bennett, D Ackerman, W Park, J Bogovic… - bioRxiv, 2020‏ - biorxiv.org
Cells contain hundreds of different organelle and macromolecular assemblies intricately
organized relative to each other to meet any cellular demands. Obtaining a complete …

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

H Spiers, H Songhurst, L Nightingale, J de Folter… - bioRxiv, 2020‏ - biorxiv.org
Advancements in volume electron microscopy mean it is now possible to generate
thousands of serial images at nanometre resolution overnight, yet the gold standard …

CebraEM: a practical workflow to segment cellular organelles in volume SEM datasets using a transferable CNN-based membrane prediction

J Hennies, JMS Lleti, C Pape, S Bekbayev, V Gross… - bioRxiv, 2023‏ - biorxiv.org
Segmentation of large-volume datasets obtained by volume SEM techniques is a
challenging task that generally requires a considerable amount of human effort. Despite …

An effective encoder-decoder network for neural cell bodies and cell nucleus segmentation of EM images

Y Jiang, C **ao, L Li, X Chen, L Shen… - 2019 41st Annual …, 2019‏ - ieeexplore.ieee.org
Neural systems are complicated networks connected by a large number of neurons through
gap junctions and synapse. At present, for electron microscopy connectomics research …

Modified UNet architecture with less number of learnable parameters for nuclei segmentation

S Vishnu Priyal, MT Vyshnav, V Sowmya… - Soft Computing and …, 2022‏ - Springer
The analysis of cell nuclei plays a vital role in the field of pathology. The process of
identifying the cell nuclei is considered difficult due to several challenges. In this work, we …

Efficient nucleus detection in digital pathology images using multi-task and multi-scale instance segmentation network

M Sun, H Dang, GH Zhang, Z Yao… - 2019 International …, 2019‏ - ieeexplore.ieee.org
Automatic cell spotting is a challenging problem in biomedical image analysis. Efficient
detection of the nuclei in these cells is important for both clinicians and researchers …

Automated segmentation of immunostained cell nuclei in 3D ultramicroscopy images

A Scherzinger, F Kleene, C Dierkes, F Kiefer… - … , GCPR 2016, Hannover …, 2016‏ - Springer
Detection, segmentation, and quantification of individual cell nuclei is a standard task in
biomedical applications. Due to the increasing volume of acquired image data, it is not …