Data and Tools
The laboratory develops database applications for image data, methods for computerized data acquisition, 3-D reconstruction, visualization and quantitative analyses of large neuronal populations and brain regions in the mammalian brain.
The methods are employed to investigate the architecture of large projection systems in the mammalian brain, as well as to study whole brain distribution patterns for gene, molecular,and circuit level data.
Database applications developed by our laboratory are presented via The Rodent Brain WorkBench.
NeSys has developed software for 3-D reconstruction, visualization, and analysis of nerve cell populations and brain regions, based on point and line coded data from serial sections. This software has been used in more than 25 publications, in species ranging from insects to monkeys, in multiple laboratories in Europe, USA, and Asia.
NeSys has used programme AnalySIS (Soft Imaging System GmbH, Münster, Germany) for some of its publications. These tutorials explain basic AnalySIS interface and features, and examplify the use of AnalySIS for image analysis purposes.
- Basic AnalySIS tutorial (pdf.)
- Using AnalySIS® to detect cells and collect data from a Fluororuby-stained section (pdf.)
This last tutorial describes how to separate stained elements from background, separate cells from artefacts, detect the cells and in the end get a list with xy-coordinates (and other relevant info) on each cell.