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

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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.