• Publications
  • Influence
Fiji: an open-source platform for biological-image analysis
TLDR
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. Expand
ImageJ2: ImageJ for the next generation of scientific image data
TLDR
The entire ImageJ codebase was rewrote, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. Expand
The ImageJ ecosystem: An open platform for biomedical image analysis
TLDR
The ImageJ project is used as a case study of how open‐source software fosters its suites of software tools, making multitudes of image‐analysis technology easily accessible to the scientific community. Expand
TrackMate: An open and extensible platform for single-particle tracking.
TLDR
TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment and is validated for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells. Expand
A new metric for probability distributions
We introduce a metric for probability distributions, which is bounded, information-theoretically motivated, and has a natural Bayesian interpretation. The square root of the well-known /spl chi//supExpand
TrakEM2 Software for Neural Circuit Reconstruction
TLDR
A software application, TrakEM2, is designed that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes and addresses the challenges of image volume composition from individual, deformed images. Expand
Crowdsourcing the creation of image segmentation algorithms for connectomics
To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain.Expand
A high-level 3D visualization API for Java and ImageJ
TLDR
This framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment and provides high-level access to volume rendering, volume editing, surface extraction, and image annotation. Expand
Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification
TLDR
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, is introduced. Expand
Software for bead-based registration of selective plane illumination microscopy data
TLDR
It is shown here how bead-based and intensity-based multi-view reconstruction on 7-view acquisition of Drosophila embryo expressing His-YFP affects the registration error of the SPIM registration plugin. Expand
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