Software tools for automated transmission electron microscopy

M Schorb, I Haberbosch, WJH Hagen, Y Schwab… - Nature …, 2019 - nature.com
The demand for high-throughput data collection in electron microscopy is increasing for
applications in structural and cellular biology. Here we present a combination of software …

Analysis of clonogenic growth in vitro

N Brix, D Samaga, C Belka, H Zitzelsberger… - Nature protocols, 2021 - nature.com
The clonogenic assay measures the capacity of single cells to form colonies in vitro. It is
widely used to identify and quantify self-renewing mammalian cells derived from in vitro …

OpenCell: Endogenous tagging for the cartography of human cellular organization

NH Cho, KC Cheveralls, AD Brunner, K Kim… - Science, 2022 - science.org
Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era.
We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data …

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

L Manubens-Gil, Z Zhou, H Chen, A Ramanathan… - Nature …, 2023 - nature.com
BigNeuron is an open community bench-testing platform with the goal of setting open
standards for accurate and fast automatic neuron tracing. We gathered a diverse set of …

[HTML][HTML] Characterizing microglia activation: a spatial statistics approach to maximize information extraction

BM Davis, M Salinas-Navarro, MF Cordeiro, L Moons… - Scientific reports, 2017 - nature.com
Microglia play an important role in the pathology of CNS disorders, however, there remains
significant uncertainty about the neuroprotective/degenerative role of these cells due to a …

High-definition imaging using line-illumination modulation microscopy

Q Zhong, A Li, R **, D Zhang, X Li, X Jia, Z Ding… - Nature …, 2021 - nature.com
The microscopic visualization of large-scale three-dimensional (3D) samples by optical
microscopy requires overcoming challenges in imaging quality and speed and in big data …

Whole-neuron synaptic map** reveals spatially precise excitatory/inhibitory balance limiting dendritic and somatic spiking

DM Iascone, Y Li, U Sümbül, M Doron, H Chen… - Neuron, 2020 - cell.com
The balance between excitatory and inhibitory (E and I) synapses is thought to be critical for
information processing in neural circuits. However, little is known about the spatial principles …

A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei

JM Phillip, KS Han, WC Chen, D Wirtz, PH Wu - Nature protocols, 2021 - nature.com
Cell morphology encodes essential information on many underlying biological processes. It
is commonly used by clinicians and researchers in the study, diagnosis, prognosis, and …

Image-based cell phenoty** with deep learning

A Pratapa, M Doron, JC Caicedo - Current opinion in chemical biology, 2021 - Elsevier
A cell's phenotype is the culmination of several cellular processes through a complex
network of molecular interactions that ultimately result in a unique morphological signature …

[HTML][HTML] A bird's-eye view of deep learning in bioimage analysis

E Meijering - Computational and structural biotechnology journal, 2020 - Elsevier
Deep learning of artificial neural networks has become the de facto standard approach to
solving data analysis problems in virtually all fields of science and engineering. Also in …