Exploring the numerical results

In the test_brain/output/analysis directory is a summary.csv file which you can open in Microsoft Excel (or similar) to view a summary of the results. This file lists (for each brain area); the number of cells detected, the volume of the brain area, and the density of cells (in cells per mm³). This is the file you’ll most likely use for statistical analysis. It will look something like this (but with an entry for each brain area):

structure_name	left_cell_count	right_cell_count	total_cells	left_volume_mm3	right_volume_mm3	total_volume_mm3	left_cells_per_mm3	right_cells_per_mm3
Retrosplenial area, ventral part, layer 5	1853	814	2667	0.952479	0.966508	1.918987	1945.44971595174	842.207203665153
Lateral dorsal nucleus of thalamus	1541	0	1541	0.597768	0.534717	1.132485	2577.92320766585	0
Retrosplenial area, ventral part, layer 2/3	163	686	849	0.57638	0.614387	1.190767	282.79954196884	1116.56008346531
Retrosplenial area, dorsal part, layer 5	561	82	643	0.611487	0.644904	1.256391	917.435693645163	127.150707702232
Retrosplenial area, dorsal part, layer 2/3	194	245	439	0.460668	0.492384	0.953052	421.127579949117	497.579125235589
Ventral anterior-lateral complex of the thalamus	412	0	412	0.397422	0.365181	0.762603	1036.6814116984	0

These data allow you to compare data from multiple samples. To visualise data from different samples in the same coordinate space, take a look at Visualising your data in brainrender.