Zfish_recon

Contains scripts to analyze the reconstructions from the hindbrain dataset.

These scripts were used for the pre-print https://www.biorxiv.org/content/10.1101/2020.10.28.359620v3.
Requires the installation of the treestoolbox (https://www.mathworks.com/matlabcentral/fileexchange/68886-trees-toolbox/) developed by Hermann Cuntz.
Required Statistics and Machine Learning provided by mathworks
Some hardcoded paths in the scrips might need to be updated before running the scripts.
\scripts - contains all the scripts needed to generate the figures in the pre-print. - Third party scripts provided are colorcet.m, adjustedRandIndex.m, compute_confusion.m, VOI.m, locallog,m
\matFiles - Important .matFiles, are used in analysis and figures. - -Run multiScaleModularity.m before plotMultiScaleModularity.m or modularityScaling_500_OM_0_01_cleaned.mat
\skeletons - contains most if not all skeletons used for analysis in the paper. Any missing skeletons will be preserved in the private google drive folder used by the lab.
fig_mFiles - contains some of the m files, that generate the figures from the manuscript.

Terminology

scw is the common extension for representing neuronal skeletons.
- Root - root node of the tree, typically is the soma. For trees without somas in the reconstructed volume, the first plane of the 3D volume is considered as the root node.
Zbrain - refers to the Zbrain atals for larval zebrafish developed by the Engert lab.