• Publications
  • Influence
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 libraries with aExpand
  • 25,054
  • 2495
  • PDF
TrakEM2 Software for Neural Circuit Reconstruction
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 acquisition of imageryExpand
  • 593
  • 45
  • PDF
A multilevel multimodal circuit enhances action selection in Drosophila
We show that combining mechanosensory and nociceptive cues synergistically enhances the selection of the fastest mode of escape locomotion in Drosophila larvae. Expand
  • 289
  • 30
  • PDF
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 serialExpand
  • 319
  • 29
  • PDF
Crowdsourcing the creation of image segmentation algorithms for connectomics
We propose a solution to this problem, which should be useful for a future 3D segmentation challenge. Expand
  • 222
  • 28
  • PDF
Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification
We have introduced the Trainable Weka Segmentation (TWS), a machine learning tool that leverages a limited number of manual annotations in order to train a classifier and segment the remaining data automatically. Expand
  • 603
  • 27
A high-level 3D visualization API for Java and ImageJ
We present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Expand
  • 379
  • 21
  • PDF
The complete connectome of a learning and memory centre in an insect brain
We provide the first complete wiring diagram of a parallel fiber circuit for adaptive behavioral control in the Drosophila larval mushroom body. Expand
  • 267
  • 20
  • PDF
Quantitative neuroanatomy for connectomics in Drosophila
Neuronal circuit mapping using electron microscopy demands laborious proofreading or reconciliation of multiple independent reconstructions. Here, we describe new methods to apply quantitative arborExpand
  • 187
  • 19
  • PDF
CATMAID: collaborative annotation toolkit for massive amounts of image data
We present here a decentralized web interface, modeled after GoogleMaps™, to navigate large multidimensional biological image datasets and collaboratively annotate features in them. Expand
  • 237
  • 18
  • PDF