248 citations · 513 across the 11 of their papers we have counts for
13 papers
Graph neural networks uncover structure and functions underlying the activity of simulated neural assemblies
Cédric Allier, Larissa Heinrich, Magdalena Schneider +1
Graph neural networks trained to predict observable dynamics can be used to decompose the temporal activity of complex heterogeneous systems into simple, interpretable representati…
DeepPD: Joint Phase and Object Estimation from Phase Diversity with Neural Calibration of a Deformable Mirror
Magdalena C. Schneider, Courtney Johnson, Cedric Allier +6
Sample-induced aberrations and optical imperfections limit the resolution of fluorescence microscopy. Phase diversity is a powerful technique that leverages complementary phase inf…
Decomposing heterogeneous dynamical systems with graph neural networks
Cédric Allier, Magdalena C. Schneider, Michael Innerberger +3
Natural physical, chemical, and biological dynamical systems are often complex, with heterogeneous components interacting in diverse ways. We show how simple graph neural networks…
SciJava Ops: An Improved Algorithms Framework for Fiji and Beyond
Gabriel J. Selzer, Curtis T. Rueden, Mark C. Hiner +13
Many scientific software platforms provide plugin mechanisms that simplify the integration, deployment, and execution of externally developed functionality. One of the most widely…
Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain
Larissa Heinrich, Jan Funke, Constantin Pape +2
Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron…
Joint Deformable Registration of Large EM Image Volumes: A Matrix Solver Approach
Khaled Khairy, Gennady Denisov, Stephan Saalfeld
Large electron microscopy image datasets for connectomics are typically composed of thousands to millions of partially overlapping two-dimensional images (tiles), which must be reg…
Large Scale Image Segmentation with Structured Loss based Deep Learning for Connectome Reconstruction
Jan Funke, Fabian David Tschopp, William Grisaitis +4
We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy…
The Candidate Multi-Cut for Cell Segmentation
Jan Funke, Chong Zhang, Tobias Pietzsch +1
Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by so…
Deep Learning for Isotropic Super-Resolution from Non-Isotropic 3D Electron Microscopy
Larissa Heinrich, John A. Bogovic, Stephan Saalfeld
The most sophisticated existing methods to generate 3D isotropic super-resolution (SR) from non-isotropic electron microscopy (EM) are based on learned dictionaries. Unfortunately,…
Robust Registration of Calcium Images by Learned Contrast Synthesis
John A. Bogovic, Philipp Hanslovsky, Allan Wong +1
Multi-modal image registration is a challenging task that is vital to fuse complementary signals for subsequent analyses. Despite much research into cost functions addressing this…
Image-Based Correction of Continuous and Discontinuous Non-Planar Axial Distortion in Serial Section Microscopy
Philipp Hanslovsky, John A. Bogovic, Stephan Saalfeld
Motivation: Serial section microscopy is an established method for detailed anatomy reconstruction of biological specimen. During the last decade, high resolution electron microsco…
BigDataViewer: Interactive Visualization and Image Processing for Terabyte Data Sets
Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch +1
The increasingly popular light sheet microscopy techniques generate very large 3D time-lapse recordings of living biological specimen. The necessity to make large volumetric datase…
Post-acquisition image based compensation for thickness variation in microscopy section series
Philipp Hanslovsky, John A. Bogovic, Stephan Saalfeld
Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction…