**Overview**
Files within this project are the data and analysis tools for "Spatial models of cell distribution in human dorsal root ganglia", published by the Journal of Comparative Neurology (https://onlinelibrary.wiley.com/doi/full/10.1002/cne.24848). Folders in the repository are described below
*Note: As of 1/6/2020, all raw images are available, but upload of analysis tools and summary spreadsheets is pending. This will be rectified shortly and this notice removed. Please contact the authors with any questions at bruns@umich.edu*
**Summary Spreadsheets**
This folder will contain spreadsheets which describe individual experiments and trials at a high level.
*cells_all_final.*
*cells_all_final_good.*
*density_table_final_z.xlsx*
*region_areas_human_drg_all.xlsc*
**SVS**
svs files originally contained seven layers
1-5: image files of varying resolution
6:macroscopic image of slide label
7: macroscopic image of entire slide
This folder contains the histological images . These images are taken from the highest resolution image from the original svs. The files follow the format *donor#-root-direction-slice#* The donor number must contain two digits (02). The root contains R or L for right or left, followed by the vertebra name. The direction must be either dist to denote the side distal to the sample's initial bisection, or prox for proximal. Slice number describes the location of the slice within each DRG half, with 1 being closest to the initial bisection, this contains 3 digits (001).
Example 02-RL5-Prox-003
**MATLAB Files**
This folder contains scripts and functions required to reproduce the results and figures in Sperry et al. All files should be placed in the same directory. MATLAB 2019a is recommended.
The scripts contain descriptions of their functionality and required inputs within the code comments
DRG3DAnalysis.m
DRG3DAnalysis.fig
PerimVal.m
PolarBuilder.m
The toolboxes 'Image Processing Toolbox' and 'Statistics and Machine Learning Toolbox' are required as well.
**Flux Input**
This folder contains .mat files containing preprocessing data. All files follow the format *slicename-ToFlux.mat*.
The file contains three structure: VR, DRG, and Epinurium, which all contain binary images corresponding to each element. The cell array pics contains the original, and rotated (if applicable) versions of the svs. The file also contains FileName, the slice name.
**Flux Output**
This folder contains .mat file pairs containing postprocessing data. All file pairs follow the format *slicename-FluxOut.mat* and *slicename-FluxOutNorm.mat*
The first file contains *DRG_centroid_table*, a table that list the centroid, Minor and Major Axes, eccentricity, area, normalized radius, angle, and weather a nucleus is present for each cell within the DRG labeled. *VR_centroid_table* contains the same data for elements within the VR, sans nuclei data.
*DRG_norm_by_cell*
*DRG_pixels_by_cell*
*VR_norm_by_cell*
*VR_pixels_by_cell*
and the file name.
The second file contains the file name as well as *DRG_centroids_norm* and *VR_centroids_norm* which contain the radii and angle of normalized elements within the DRG and VR respectivly.
