239 citations · 253 across the 9 of their papers we have counts for
11 papers · 1 filter
Catena: A Comprehensive Software Suite for Large-Scale Connectomics
Samia Mohinta, Pedro Gómez-Gálvez, Shi Yan Lee +5
The gold standard datasets for mapping connectomes are electron microscopy volumes of densely labeled neural tissue at nanometer resolution. Yet reconstructing and proofreading neu…
Tracking by weakly-supervised learning and graph optimization for whole-embryo C. elegans lineages
Peter Hirsch, Caroline Malin-Mayor, Anthony Santella +3
Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-super…
How Shift Equivariance Impacts Metric Learning for Instance Segmentation
Josef Lorenz Rumberger, Xiaoyan Yu, Peter Hirsch +6
Metric learning has received conflicting assessments concerning its suitability for solving instance segmentation tasks. It has been dismissed as theoretically flawed due to the sh…
Microtubule Tracking in Electron Microscopy Volumes
Nils Eckstein, Julia Buhmann, Matthew Cook +1
We present a method for microtubule tracking in electron microscopy volumes. Our method first identifies a sparse set of voxels that likely belong to microtubules. Similar to prior…
Instance Separation Emerges from Inpainting
Steffen Wolf, Fred A. Hamprecht, Jan Funke
Deep neural networks trained to inpaint partially occluded images show a deep understanding of image composition and have even been shown to remove objects from images convincingly…
Synaptic partner prediction from point annotations in insect brains
Julia Buhmann, Renate Krause, Rodrigo Ceballos Lentini +4
High-throughput electron microscopy allows recording of lar- ge stacks of neural tissue with sufficient resolution to extract the wiring diagram of the underlying neural network. C…
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…
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…
TED: A Tolerant Edit Distance for Segmentation Evaluation
Jan Funke, Francesc Moreno-Noguer, Albert Cardona +1
In this paper, we present a novel error measure to compare a segmentation against ground truth. This measure, which we call Tolerant Edit Distance (TED), is motivated by two observ…
Multi-Hypothesis CRF-Segmentation of Neural Tissue in Anisotropic EM Volumes
Jan Funke, Björn Andres, Fred Hamprecht +2
We present an approach for the joint segmentation and grouping of similar components in anisotropic 3D image data and use it to segment neural tissue in serial sections electron mi…