WholeBrain

Structural and functional mapping of neural circuits at a whole-brain level is an emerging area in neuroscience, with projects around the world attempting to map the mouse brain by cell type, activity, long and short term connectivity patterns, and circuit interactions. The Whole Brain project is a well-developed tool for this kind of mapping. It was developed by Daniel Fürth in Konstantinos Meletis’ research group at the Karolinska Institutet. The Whole Brain project is a computational framework based on two open-source packages, WholeBrain and OpenBrainMap. This software has combined multiple connectivity projects (all based off of light microscopy) to create the aforementioned projects to create an accessible and standardized tool to allow for large-scale whole-brain mapping projects. Written in C++, the program is importable and usable in R, JavaScript, and WASM. In addition, maps are exportable and viewable in standard internet browsers, making the framework accessible and understandable for all researchers. This framework revolutionizes the way neuroscientific data is visualized and shared, and allows for the quantitative analysis of microscopy

The WholeBrain package allows users to create accurate anatomical maps of multidimensional data, enabling spatial and quantitative mapping, statistical analysis, and different format outputs. The OpenBrainMap package is often used in conjunction to create interactive maps which are usable and shareable between labs. It features the ability to statistically analyze and plot anatomical differences, segment activity by neuron type, identify cortical and subcortical connections, and more. The program is applicable with data collected through light microscopy, and compatible with many imaging systems (including light-sheet, widefield, and confocal imaging) and many markings (including immunohistochemical and fluorescent protein tagging). Thus, this framework is useful for generating maps drug responses, functional connectivity, protein expression, neuron activity, etc. WholeBrain enables clear visualization and comparison of cognitive, anatomical, and behavioral functional data.

This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications. RRID: SCR_015245

Special thanks to Andra Mutu, a neuroscience undergraduate at American University, for providing this project summary.