Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy. Parts of the method are detailed in [1] where bcfind was applied to the localization of Purkinje cells in a whole mouse cerebellum.

For documentation, please see the bcfind page at DINFO, Università di Firenze.

Release 1.1 includes several improvements. In particular:

• Cell detection is significantly faster
• Support of multiview images with a hierarchical registration pipeline and Multiview Semantic Deconvolution (MSD).

The method for multiview images is described in [2] Where it has been applied to the extraction of the activation map in a whole Arc-dVenus mouse brain.

[1] Frasconi, P., Silvestri, L., Soda, P., Cortini, R., Pavone, F. S., & Iannello, G. (2014). Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images. Bioinformatics, 30(17), i587–i593. http://doi.org/10.1093/bioinformatics/btu469.

[2] Paciscopi, M., Silvestri, L., Pavone, F.S., & Frasconi, P. (2015). Cell identification in whole-brain multiview images of neural activation maps. http://arxiv.org/abs/1511.01168.