Appendix 7—table 3. Comparison between 2D vs 3D super pixels.

From out experiments, segmentation quality is almost always improved by the usage of 3D super pixels. On the other side, the user should be aware that this improvement comes at the cost of a large slow-down of the pipeline (roughly × 4.5 on our system Intel Xenon E5-2660, RAM 252 Gb).

ds3 confocal + rescaling
Over/under factor 0.7
Dataset	Super Pixels 2D (Default)				Super Pixels 3D
	ARand	VOIsplit	VOImerge	time (s)	ARand	VOIsplit	VOImerge	time (s)
Anther	0.215	1.130	0.517	600	0.167	0.787	0.399	2310
Filament	0.159	0.899	0.350	120	0.171	0.687	0.487	520
Leaf	0.117	0.502	0.247	800	0.080	0.308	0.220	3650
Pedicel	0.339	1.148	0.894	450	0.314	0.845	0.604	2120
Root	0.113	0.672	0.485	210	0.101	0.356	0.412	920
Sepal	0.346	0.926	1.211	770	0.257	0.690	0.966	3420
Valve	0.444	0.828	1.138	530	0.300	0.494	0.875	2560
Average	0.248	0.872	0.691	500	0.199	0.595	0.566	2210