Fiji: an open-source platform for biological-image analysis

J Schindelin, I Arganda-Carreras, E Frise, V Kaynig… - Nature …, 2012 - nature.com
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image
analysis. Fiji uses modern software engineering practices to combine powerful software …

Polymerization shrinkage assessment of dental resin composites: a literature review

D Kaisarly, ME Gezawi - Odontology, 2016 - Springer
Composite restorations are widely used worldwide, but the polymerization shrinkage is their
main disadvantage that may lead to clinical failures and adverse consequences. This review …

Deep learning in medical image registration: a survey

G Haskins, U Kruger, P Yan - Machine Vision and Applications, 2020 - Springer
The establishment of image correspondence through robust image registration is critical to
many clinical tasks such as image fusion, organ atlas creation, and tumor growth monitoring …

Shrinkage-mediated imaging of entire organs and organisms using uDISCO

C Pan, R Cai, FP Quacquarelli, A Ghasemigharagoz… - Nature …, 2016 - nature.com
Recent tissue-clearing approaches have become important alternatives to standard
histology approaches. However, light scattering in thick tissues and the size restrictions on …

TrakEM2 software for neural circuit reconstruction

A Cardona, S Saalfeld, J Schindelin… - PloS one, 2012 - journals.plos.org
A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For
model systems such as Drosophila and C. elegans, the limiting step is no longer the …

Virtual alignment of pathology image series for multi-gigapixel whole slide images

CD Gatenbee, AM Baker, S Prabhakaran… - Nature …, 2023 - nature.com
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains
challenging, due to cost, expertise, methodical constraints, and access to technology. An …

3D reconstruction of histological sections: Application to mammary gland tissue

I Arganda‐Carreras… - Microscopy research …, 2010 - Wiley Online Library
In this article, we present a novel method for the automatic 3D reconstruction of thick tissue
blocks from 2D histological sections. The algorithm completes a high‐content (multiscale …

A cellular resolution atlas of Broca's area

I Costantini, L Morgan, J Yang, Y Balbastre… - Science …, 2023 - science.org
Brain cells are arranged in laminar, nuclear, or columnar structures, spanning a range of
scales. Here, we construct a reliable cell census in the frontal lobe of human cerebral cortex …

[HTML][HTML] A modular platform for automated cryo-FIB workflows

S Klumpe, HKH Fung, SK Goetz, I Zagoriy, B Hampoelz… - Elife, 2021 - ncbi.nlm.nih.gov
Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB)
has matured into a preparation method widely used for cellular cryo-electron tomography …

ANHIR: automatic non-rigid histological image registration challenge

J Borovec, J Kybic, I Arganda-Carreras… - IEEE transactions on …, 2020 - ieeexplore.ieee.org
Automatic Non-rigid Histological Image Registration (ANHIR) challenge was organized to
compare the performance of image registration algorithms on several kinds of microscopy …