Table 2.

Three-channel imaging and detection of indicated molecule combinations

Channel wavelengthPSF sigma (pixels, nm)Parameters
TfR/TSAd/CHC 
TfR 561 1.4, 113 Alpha: 0.01, all others: default 
TSAd 488 1.2, 97 Alpha: 0.01, all others: default 
CHC 640 1.58, 128 Alpha: 0.05, all others: default 
Activated β1-integrin/pFAK/paxillin 
Activated β1-integrin 561 1.4, 113 Alpha: 0.01, all others: default 
pFAK 488 1.2, 97 Alpha: 0.01, all others: default 
Paxillin 640 N/A N/A 
VEGFR-2/TSAd/CHC 
VEGFR-2 561 1.4, 113 Alpha: 0.05, all others: default 
TSAd 488 1.2, 97 Alpha: 0.01, all others: default 
CHC 640 1.58, 128 Alpha: 0.05, all others: default 
VEGFR-2/TSAd/paxillin 
VEGFR-2 561 1.4, 113 Alpha: 0.05, all others: default 
TSAd 488 1.2, 97 Alpha: 0.01, all others: default 
Paxillin 640 N/A N/A 
Channel wavelengthPSF sigma (pixels, nm)Parameters
TfR/TSAd/CHC 
TfR 561 1.4, 113 Alpha: 0.01, all others: default 
TSAd 488 1.2, 97 Alpha: 0.01, all others: default 
CHC 640 1.58, 128 Alpha: 0.05, all others: default 
Activated β1-integrin/pFAK/paxillin 
Activated β1-integrin 561 1.4, 113 Alpha: 0.01, all others: default 
pFAK 488 1.2, 97 Alpha: 0.01, all others: default 
Paxillin 640 N/A N/A 
VEGFR-2/TSAd/CHC 
VEGFR-2 561 1.4, 113 Alpha: 0.05, all others: default 
TSAd 488 1.2, 97 Alpha: 0.01, all others: default 
CHC 640 1.58, 128 Alpha: 0.05, all others: default 
VEGFR-2/TSAd/paxillin 
VEGFR-2 561 1.4, 113 Alpha: 0.05, all others: default 
TSAd 488 1.2, 97 Alpha: 0.01, all others: default 
Paxillin 640 N/A N/A 

PSF, point spread function. Shown are the parameters of the “point-source detection” particle detection algorithm in u-track that vary between channels and datasets. Two other parameters that change (namely “Max Fit Adjust” and “Fit Window Size”) are not shown because they were given their default values of 2 × PSF sigma and 4 × PSF sigma, respectively. The paxillin channel has N/A parameters because it was not detected using point-source detection due to its non-punctate nature.

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