Fiji: an open-source platform for biological-image analysis
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 …
analysis. Fiji uses modern software engineering practices to combine powerful software …
Globally optimal stitching of tiled 3D microscopic image acquisitions
Motivation: Modern anatomical and developmental studies often require high-resolution
imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-…
imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-…
A connectome and analysis of the adult Drosophila central brain
The neural circuits responsible for animal behavior remain largely unknown. We summarize
new methods and present the circuitry of a large fraction of the brain of the fruit fly …
new methods and present the circuitry of a large fraction of the brain of the fruit fly …
[HTML][HTML] TrakEM2 software for neural circuit reconstruction
… Indeed, ever since Schwann’s theory of the cell and Cajal’s neuron doctrine, neuroscientists
have struggled to describe the diversity of neurons in the brain and their synaptic contacts …
have struggled to describe the diversity of neurons in the brain and their synaptic contacts …
[PDF][PDF] A complete electron microscopy volume of the brain of adult Drosophila melanogaster
… dose rate required for a 2 s exposure on Kodak 4489 film at 120 kV) to saturate the sensor
wells within the short interval (35 ms in our case, versus $1 - 2 s typical integration time). Pre-…
wells within the short interval (35 ms in our case, versus $1 - 2 s typical integration time). Pre-…
Animal behavior in urban ecosystems: modifications due to human-induced stress
SS Ditchkoff, ST Saalfeld, CJ Gibson - Urban ecosystems, 2006 - Springer
Wildlife-human interactions are increasing in prevalence as urban sprawl continues to
encroach into rural areas. Once considered to be unsuitable habitat for most wildlife species, …
encroach into rural areas. Once considered to be unsuitable habitat for most wildlife species, …
A review on the reliability of hemodynamic modeling in intracranial aneurysms: why computational fluid dynamics alone cannot solve the equation
P Berg, S Saalfeld, S Voß, O Beuing, G Janiga - Neurosurgical focus, 2019 - thejns.org
… Behrendt B, Berg P, Beuing O, Preim B, Saalfeld S: Explorative blood flow visualization using
dynamic line filtering based on surface features. Comput Graph Forum 37:183– 194, 2018 …
dynamic line filtering based on surface features. Comput Graph Forum 37:183– 194, 2018 …
Whole-cell organelle segmentation in volume electron microscopy
…, W Korff, HF Hess, J Lippincott-Schwartz, S Saalfeld… - Nature, 2021 - nature.com
… & Saalfeld, S. Synaptic cleft segmentation in non-isotropic volume electron microscopy of
the complete Drosophila brain. In Medical Image Computing and Computer Assisted …
the complete Drosophila brain. In Medical Image Computing and Computer Assisted …
Software for bead-based registration of selective plane illumination microscopy data
To the Editor: Selective plane illumination microscopy (SPIM) 1 allows isotropic, time-lapse,
in toto imaging of large, living biological specimens by acquiring three-dimensional (3D) …
in toto imaging of large, living biological specimens by acquiring three-dimensional (3D) …
[HTML][HTML] An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy
The analysis of microcircuitry (the connectivity at the level of individual neuronal processes
and synapses), which is indispensable for our understanding of brain function, is based on …
and synapses), which is indispensable for our understanding of brain function, is based on …