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The resultant dataset was a non-negative matrix, which was subject to gNMF using a custom software package [17] and run in MATLAB (The MathWorks, Inc., Natick, MA).
Expressed Affymetrix probes on the 430v2 chip were batch queried to NetAffx raw data (release 21) using a custom software application (J.
The eyetracker, the ViSaGe, and the screen were synchronized using a custom software interface.
Averaged frames were analysed using a custom software written in MATLAB.
Renormalized (quantile) LRR and BAF values were then analyzed using a custom software pipeline, R-Gada [ 27], to detect whole-chromosome and segmental events as previously described [ 28].
Data pre-processing, detection of repeated visits by the same patient for the same syndrome, and data aggregation is performed using a custom software package, written, maintained, and distributed by the NDP datacenter.
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Other approaches include LMD (Mobile Assay, CO, USA), whom use a custom software application running on a cell phone.
Phase-contrast images were segmented using a custom MATLAB software package called Morphometrics, as in Ursell et al. (2014).
Carotid lumen and vessel wall area was measured using a custom designed software program.
Ultrasound images of 24 high-risk and 32 low-risk carotid plaques were manually segmented by an experienced physician using a custom developed software.
Ultrasound images of 154 confirmed lesions (59 benign and 52 malignant solid masses, 7 simple cysts, and 32 complicated cysts) were manually segmented by a physician using a custom developed software.
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