Table 1. Timing of the entire pipeline for a zebrafish patch.

CNMF method	[8]	here & [18]
load data†	22 ± 1	22 ± 1
decimate	N/A	33 ± 1
detect ROIs‡	5,360 ± 20	135 ± 2
NMF	35,100 ± 400	990 ± 10
ΔF/F	410 ± 10	410 ± 10
denoise	17,900 ± 300	600 ± 20

Average computing time (± SEM) in ms over ten runs for individual steps of the processing pipeline on a standard laptop. The 96×96 patch contained N = 46 neurons recorded for T = 3000 frames.

^†Loading the whole data as single binary file; loading a frame at a time was an order of magnitude slower.

^‡Using greedy initialization; group lasso initialization [8] was an order of magnitude slower.