[HTML][HTML] D-LMBmap: a fully automated deep-learning pipeline for whole-brain profiling of neural circuitry

Z Li, Z Shang, J Liu, H Zhen, E Zhu, S Zhong… - Nature …, 2023 - nature.com
Recent proliferation and integration of tissue-clearing methods and light-sheet fluorescence
microscopy has created new opportunities to achieve mesoscale three-dimensional whole …

High-contrast en bloc staining of mouse whole-brain and human brain samples for EM-based connectomics

K Song, Z Feng, M Helmstaedter - Nature Methods, 2023 - nature.com
Connectomes of human cortical gray matter require high-contrast homogeneously stained
samples sized at least 2 mm on a side, and a mouse whole-brain connectome requires …

Quantum Neurobiology

M Swan, RP dos Santos, F Witte - Quantum Reports, 2022 - mdpi.com
Quantum neurobiology is concerned with potential quantum effects operating in the brain
and the application of quantum information science to neuroscience problems, the latter of …

RoboEM: automated 3D flight tracing for synaptic-resolution connectomics

M Schmidt, A Motta, M Sievers, M Helmstaedter - Nature Methods, 2024 - nature.com
Mapping neuronal networks from three-dimensional electron microscopy (3D-EM) data still
poses substantial reconstruction challenges, in particular for thin axons. Currently available …

Generative and discriminative model-based approaches to microscopic image restoration and segmentation

S Ishii, S Lee, H Urakubo, H Kume, H Kasai - Microscopy, 2020 - academic.oup.com
Image processing is one of the most important applications of recent machine learning (ML)
technologies. Convolutional neural networks (CNNs), a popular deep learning-based ML …

Sparse projection oblique randomer forests

TM Tomita, J Browne, C Shen, J Chung… - Journal of machine …, 2020 - jmlr.org
Decision forests, including Random Forests and Gradient Boosting Trees, have recently
demonstrated state-of-the-art performance in a variety of machine learning settings …

Graph partitioning algorithms with biological connectivity decisions for neuron reconstruction in electron microscope volumes

B Hong, J Liu, L Shen, Q Xie, J Yuan… - Expert Systems with …, 2023 - Elsevier
Neuron reconstruction algorithms used in electron microscope volumes have received
increasing attention in recent years. Most current methods are highly reliant on neuron …

Dendritic spine density scales with microtubule number in rat hippocampal dendrites

KM Harris, DD Hubbard, M Kuwajima, WC Abraham… - Neuroscience, 2022 - Elsevier
Microtubules deliver essential resources to and from synapses. Three-dimensional
reconstructions in rat hippocampus reveal a sampling bias regarding spine density that …

MTNeuro: a benchmark for evaluating representations of brain structure across multiple levels of abstraction

J Quesada, L Sathidevi, R Liu, N Ahad… - Advances in neural …, 2022 - proceedings.neurips.cc
There are multiple scales of abstraction from which we can describe the same image,
depending on whether we are focusing on fine-grained details or a more global attribute of …

A novel 3D instance segmentation network for synapse reconstruction from serial electron microscopy images

J Liu, B Hong, C Xiao, H Zhai, L Shen, Q Xie… - Expert Systems with …, 2024 - Elsevier
Synapses are fundamental components of how neurons communicate with each other and
have attracted widespread attention from neuroscientists. Due to the rapid development of …