daniel fürth

WholeBrain is intended as a software suite, meaning a collection of computer programs sharing a common interface and ability to integrate and exchange data with each other.

The purpose of WholeBrain is to provide a user-friendly and efficient way for scientist with minimal knowledge of computers to create anatomical maps and integrate this information with behavioral and physiological data for sharing on the web.

WholeBrain is conceived and created by Daniel Fürth, during his PhD in Konstantinos Meletis lab, at Department of Neuroscience, Karolinska Institutet.

Daniel is now a postdoctoral researcher in Jay Lee's lab at Cold Spring Harbor Laboratory working on next-generation of in situ sequencing methods.


For data handling, statistical analysis and graphical plotting WholeBrain relies on R, a free software environment for statistical computing and graphics in executing commands, originally conceived and created by Ross Ihaka and Robert Gentleman.

WholeBrain handles images through OpenCV, an image processing library originally written in C and designed for computational efficiency and with a strong focus on real-time application.

To interface OpenCV with R WholeBrain uses Rcpp, by Dirk Eddelbuettel and Romain Francois, for seamless R/C++ integration.