Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

A Müller, D Schmidt, JP Albrecht, L Rieckert, M Otto… - Nature …, 2024 - nature.com
Volume electron microscopy is the method of choice for the in situ interrogation of cellular
ultrastructure at the nanometer scale, and with the increase in large raw image datasets …

Cryo-plasma FIB/SEM volume imaging of biological specimens

M Dumoux, T Glen, JLR Smith, EML Ho, LMA Perdigão… - Elife, 2023 - elifesciences.org
Serial focussed ion beam scanning electron microscopy (FIB/SEM) enables imaging and
assessment of subcellular structures on the mesoscale (10 nm to 10 µm). When applied to …

3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning

MCA Dyhr, M Sadeghi, R Moynova… - Proceedings of the …, 2023 - National Acad Sciences
Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure
of cells, offering resolution in the tens of nanometer range and strong contrast for …

Online citizen science with the Zooniverse for analysis of biological volumetric data

P Smith, ONF King, A Pennington, W Tun… - Histochemistry and Cell …, 2023 - Springer
Public participation in research, also known as citizen science, is being increasingly
adopted for the analysis of biological volumetric data. Researchers working in this domain …

An integrated approach to elucidate the interplay between iron uptake dynamics and magnetosome formation at the single-cell level in Magnetospirillum …

M Masó-Martínez, J Bond, CA Okolo… - … Applied Materials & …, 2024 - ACS Publications
Iron is a crucial element integral to various fundamental biological molecular mechanisms,
including magnetosome biogenesis in magnetotactic bacteria (MTB). Magnetosomes are …

Statistical effective diffusivity estimation in porous media using an integrated on-site imaging workflow for synchrotron users

J Le Houx, S Ruiz, D McKay Fletcher, S Ahmed… - Transport in Porous …, 2023 - Springer
Transport in porous media plays an essential role for many physical, engineering, biological
and environmental processes. Novel synchrotron imaging techniques and image-based …

Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy images

LMA Perdigão, EML Ho, ZC Cheng, NBY Yee… - Biological …, 2023 - cambridge.org
An emergent volume electron microscopy technique called cryogenic serial plasma focused
ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological …

[HTML][HTML] From Voxels to Viruses: Using Deep Learning and Crowdsourcing to Understand a Virus Factory

A Pennington, ONF King… - Citizen …, 2024 - theoryandpractice …
Many bioimaging research projects require objects of interest to be identified, located, and
then traced to allow quantitative measurement. Depending on the complexity of the system …

[PDF][PDF] Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning Models

D Bellos, M Basham - Journal of Open Source Software, 2022 - joss.theoj.org
Summary Segmentation of 3-dimensional (3D, volumetric) images is a widely used
technique that allows interpretation and quantification of experimental data collected using a …

VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles

YM Kassim, DB Rosenberg, A Renero, S Das… - …, 2024 - pmc.ncbi.nlm.nih.gov
Cochlear hair cell stereocilia bundles are key organelles required for normal hearing. Often,
deafness mutations cause aberrant stereocilia heights or morphology that are visually …