Accurately mapping the brain at the micro-scale is still a challenge in cellular neuroscience. While notable success has been reached in the field of tissue clarification and confocal imaging to obtain high-fidelity maps of three-dimensional neuron organization, neuron segmentation is still far away of ground-truth and sometimes manual segmentation performed by experts may be needed.

In this contest, we developed the Smart Region Growing algorithm (SmRG) algorithm for segmenting single neurons in their own arrangement within the brain. The algorithm performs a region growing procedure with local thresholds based on the pixel intensity statistics typical of the confocal acquisitions of biological samples and described by a mixture model. 



Please, downoad our code at It's open!