helmstaedter_to_swc

The Helmstaedter et al., Nature 2013 dataset contains thousands of skeletonizations of mouse retina in .mat format.

For some applications and analyses, the SWC format (defined here) is preferred.

The MATLAB script helmstaedter_to_swc.m, when placed in the same directory as the dataset file Helmstaedter_et_al_Nature_2013_skeletons_contacts_matrices.mat, writes all 4188 skeletons to SWC files in the same directory.

The files are named cell[cellNumber]_[skeletonNumber].swc, where cellNumber is the cellID provided by the dataset and skeletonNumber is a count of the number of skeletons written so far to the same cell.

At this time, offsets are not read from the .mat file.

Helmstaedter M, Briggman KL, Turaga S, Jain V, Seung HS, Denk W (2013). Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature, doi: 10.1038/nature12346