Electron microscopy

Estimate the positions and spacing between sections (or at local points) of three dimensional image data. This method may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2.

Super-resolve anisotropic EM data along low-res axis with deep learning.

Multicut workflow for large connectomics data. Using luigi for pipelining and caching processing steps. Most of the computations are done out-of-core using hdf5 as backend and implementations from nifty

SuRVoS: Super-Region Volume Segmentation workbench

A volume is first partitioned into Super-Regions (superpixels or supervoxels) and then interactively segmented by the user providing training annotations. SuRVoS can then learn from and extend the annotations to the whole volume.

Bigwarp is a tool for manual, interactive, landmark-based deformable image alignment. It uses the BigDataViewer for visualization and navigation, and uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.