Dense 4D nanoscale reconstruction of living brain tissue

P Velicky, E Miguel, JM Michalska, J Lyudchik, D Wei… - Nature …, 2023 - nature.com
Abstract Three-dimensional (3D) reconstruction of living brain tissue down to an individual
synapse level would create opportunities for decoding the dynamics and structure–function …

[HTML][HTML] Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset

R Conrad, K Narayan - Cell Systems, 2023 - cell.com
Mitochondria are extremely pleomorphic organelles. Automatically annotating each one
accurately and precisely in any 2D or volume electron microscopy (EM) image is an …

Current progress and challenges in large-scale 3D mitochondria instance segmentation

D Franco-Barranco, Z Lin, WD Jang… - IEEE transactions on …, 2023 - ieeexplore.ieee.org
In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance
segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI …

Imaging brain tissue architecture across millimeter to nanometer scales

JM Michalska, J Lyudchik, P Velicky… - Nature …, 2024 - nature.com
Map** the complex and dense arrangement of cells and their connectivity in brain tissue
demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels …

An overview of open source deep learning-based libraries for neuroscience

LF Tshimanga, F Del Pup, M Corbetta, M Atzori - Applied Sciences, 2023 - mdpi.com
In recent years, deep learning has revolutionized machine learning and its applications,
producing results comparable to human experts in several domains, including …

Multiplexed volumetric CLEM enabled by scFvs provides insights into the cytology of cerebellar cortex

X Han, X Lu, PH Li, S Wang, R Schalek… - Nature …, 2024 - nature.com
Map** neuronal networks is a central focus in neuroscience. While volume electron
microscopy (vEM) can reveal the fine structure of neuronal networks (connectomics), it does …

A survey of visualization and analysis in high‐resolution connectomics

J Beyer, J Troidl, S Boorboor… - Computer Graphics …, 2022 - Wiley Online Library
The field of connectomics aims to reconstruct the wiring diagram of Neurons and synapses
to enable new insights into the workings of the brain. Reconstructing and analyzing the …

Deepmulticut: Deep learning of multicut problem for neuron segmentation from electron microscopy volume

Z Li, X Yang, J Liu, B Hong, Y Zhang… - … on Pattern Analysis …, 2024 - ieeexplore.ieee.org
Superpixel aggregation is a powerful tool for automated neuron segmentation from electron
microscopy (EM) volume. However, existing graph partitioning methods for superpixel …

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

B Hong, J Liu, L Shen, Q **e, 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 …

[HTML][HTML] A robust transformer-based pipeline of 3D cell alignment, denoise and instance segmentation on electron microscopy sequence images

J Liu, Y Zheng, L Lin, J Guo, Y Lv, J Yuan, H Zhai… - Journal of Plant …, 2024 - Elsevier
Germline cells are critical for transmitting genetic information to subsequent generations in
biological organisms. While their differentiation from somatic cells during embryonic …