Single cell reconstruction data from MouseLight database and related Matlab analysis scripts

This document describes how to identify and extract ALM neurons from the MouseLight database of individual reconstructed neurons (https://ml-neuronbrowser.janelia.org/) to define ALM projection zones (relevant to Chen, Liu et al., Cell, 2023). All scripts are in Matlab R2022b.
/MouseLight_figshare/MouseLightComplete contains all reconstructed single neurons from the MouseLight data set, in .json and .swc formats.
Use ‘ExtractMouseLightNeuronsFromJsonFiles.m’ to extract MouseLight neuron ID, soma coordinates and annotation, and axon coordinates from the above directory.
Use ‘ExtractMouseLightALMneurons.m’ to identify and extract ALM neurons from the MouseLight data set. ALM neurons are defined based on functional maps of ALM (photoinhibition) in the CCF coordinate system, contained in ‘ALM_functionalData.nii’ (from Li, Daie, et al Nature, 2016).
Use ‘ALMprojDensity.m’ to compute and generate an ALM projection map based on axonal density. The map is saved in ‘ALM_mask_150um3Dgauss_Bilateral.mat’ as smoothed (3D Gaussian, sigma = 150 um) axonal density in a 3D matrix: F_smooth.
First axis: dorsal-ventral, second axis: medial-lateral, third axis: anterior-posterior.
Use ‘medial_lateral_ALMprojDensities.m’ to compute and generate medial and lateral ALM projection maps separately.
Medial ALM soma location < 1.5 mm from the midline; lateral ALM soma locations > 1.5 mm from the midline.
The maps are saved in ‘medialALM_mask_150um3Dgauss_Bilateral.mat’ and ‘lateralALM_mask_150um3Dgauss_Bilateral.mat’ as smoothed (3D Gaussian, sigma = 150 um) axonal density in 3D matrices, respectively.
Use ‘PlotALMinCCF.m’ to plot voxels of ALM in CCF, defined by the functional maps in ‘ALM_functionalData.nii’.
Use ‘PlotMouseLightALMneurons.m’ to plot ALM neurons (all, medial, or lateral) in CCF; figures are saved in .tiff format.
Other functions:
‘loadTifFast.m’ is called to load CCF .tif file (Annotation_new_10_ds222_16bit.tif).
‘plotCCFbrain.m’ is called to plot an isosurface of the CCF brain (Annotation_new_10_ds222_16bit.tif).