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Exploring the numerical results
Understanding the numerical summaries of cellfinder 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 mm^3). 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, but to visualise data from different samples in the same coordinate space, take a look at Visualising your data in brainrender.
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