Semi-automated

Integrates hardware control of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of identified regions of interest.

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.

The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy.

This project was designed for vectorize and analyze the  blood vessels in the mouse brain.

This plugin requires the definition of seed point detection settings by the user (Semi-automated).