Reconstruction of neuroanatomy is a fundamental problem in neuroscience. Stochastic expression of colors in individual cells is a promising tool, although its use in the nervous system has been limited due to various sources of variability in expression. Moreover, the intermingled anatomy of neuronal trees is challenging for existing segmentation algorithms. Here, we propose a method to automate the segmentation of neurons in such (potentially pseudo-colored) images. The method uses spatio-color relations between the voxels, generates supervoxels to reduce the problem size by four orders of magnitude before the final segmentation, and is parallelizable over the supervoxels. To quantify performance and gain insight, we generate simulated images, where the noise level and characteristics, the density of expression, and the number of fluorophore types are variable. We also present segmentations of real Brainbow images of the mouse hippocampus, which reveal many of the dendritic segments.

Reconstruction of neuroanatomy is a fundamental problem in neuroscience.

After reading the author's rebuttal I have increased the technical quality to 2 and after reading the the other reviews I increased the potential impact to 3. The authors replied to many questions but not to all, in particular the answer was not satisfactory to the question about the parameter K which is one of the crucial parameter in any segmentation algorithm. Why they did not provide the results using the suggested automatic method in Fig4 instead of cyclying on possible (wrong) number of clusters? I would have expected to see in the results the performances with at least one auto-tuning heuristic to asses its generality (at least the one suggested by the authors). In the following the issues found in the paper: 1) In Eq(2) when constructing the adjecency matrix, the ranges of the distances d(...) and \delta(...) are the same? In the line 114 d(s) is a measure of heterogeneity, in line 125 of distance and in Eq(2) of color distance.

Reconstruction of neuroanatomy is a fundamental problem in neuroscience. Stochastic expression of colors in individual cells is a promising tool, although its use in the nervous system has been limited due to various sources of variability in expression. Moreover, the intermingled anatomy of neuronal trees is challenging for existing segmentation algorithms. Here, we propose a method to automate the segmentation of neurons in such (potentially pseudo-colored) images. The method uses spatio-color relations between the voxels, generates supervoxels to reduce the problem size by four orders of magnitude before the final segmentation, and is parallelizable over the supervoxels. To quantify performance and gain insight, we generate simulated images, where the noise level and characteristics, the density of expression, and the number of fluorophore types are variable. We also present segmentations of real Brainbow images of the mouse hippocampus, which reveal many of the dendritic segments.

Reconstruction of neuroanatomy is a fundamental problem in neuroscience. Stochastic expression of colors in individual cells is a promising tool, although its use in the nervous system has been limited due to various sources of variability in expression. Moreover, the intermingled anatomy of neuronal trees is challenging for existing segmentation algorithms. Here, we propose a method to automate the segmentation of neurons in such (potentially pseudo-colored) images. The method uses spatio-color relations between the voxels, generates supervoxels to reduce the problem size by four orders of magnitude before the final segmentation, and is parallelizable over the supervoxels.

Reconstruction of neuroanatomy is a fundamental problem in neuroscience. Stochastic expression of colors in individual cells is a promising tool, although its use in the nervous system has been limited due to various sources of variability in expression. Moreover, the intermingled anatomy of neuronal trees is challenging for existing segmentation algorithms. Here, we propose a method to automate the segmentation of neurons in such (potentially pseudo-colored) images. The method uses spatio-color relations between the voxels, generates supervoxels to reduce the problem size by four orders of magnitude before the final segmentation, and is parallelizable over the supervoxels. To quantify performance and gain insight, we generate simulated images, where the noise level and characteristics, the density of expression, and the number of fluorophore types are variable. We also present segmentations of real Brainbow images of the mouse hippocampus, which reveal many of the dendritic segments.