PT  - JOURNAL ARTICLE
AU  - Alejandro Luis Callara
AU  - Chiara Magliaro
AU  - Arti Ahluwalia
AU  - Nicola Vanello
TI  - Smart Region-Growing: a novel algorithm for the segmentation of 3D clarified confocal image stacks
AID  - 10.1101/287029
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 287029
4099  - http://biorxiv.org/content/early/2018/03/22/287029.short
4100  - http://biorxiv.org/content/early/2018/03/22/287029.full
AB  - Motivation 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 manual segmentation performed by experts may be needed. The need of an expert is in part related to the limited success of the algorithms and tools performing single-neuron segmentation from 3D microscopic image data available in the State of Art, in part to the non-complete information given by these methods, which typically perform neuron tracing and thus limit the interpret-ability of results.Results In this paper, a novel algorithm for segmenting single neurons in their own arrangement within the brain is presented. The algorithm performs a region growing procedure with local thresholds based on the pixel intensity statistics typical of confocal acquisitions of biological samples and described by a mixture model. The algorithm is developed and tested on 3D confocal datasets obtained from clarified tissues. We compare the result of our algorithm with those obtained by manual segmentation performed by 6 different experts in terms of neuron surface area, volume and Sholl profiles. Statistical analysis performed on morphologic features extracted from the segmented structures confirms the feasibility of our approach.Availability The Smart Region Growing (SmRG) algorithm used in the analysis along with test confocal image stacks is available on request to the authors.Contact alejandrocallara{at}gmail.comSupplementary information Supplementary data are available on request to the authors.