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Fluorescence intensities and axon lengths were quantified using an image analysis software (SimplePCI, Compix Inc., Sewickley, PA, USA).
Actin filament lengths were quantified using the Metamorph image software.
Mean total network tubule lengths were quantified using ImageJ software.
The insert lengths were quantified using the PGF lambda ladder marker (New England Biolabs).
To investigate the effect of Gleevec on telomere length, K562, HL60, and Jurkat cells were treated with Gleevec and telomere lengths were quantified using Southern Blotting.
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Stream length, water body area, and impaired stream length were quantified using the National Hydrography Dataset and the EPA's 303 d) list.
Neurite number and length were quantified using Image Pro-Plus software.
Changes in root tip curvature and root length were quantified using the Image J program from NIH. Lateral root were quantified by counting directly under Nikon StereoZoom microscope after 5 d of transfer.
For quantitative analysis, EC nuclei number, tight junction number, pericyte cell body/process length, and EC surface length were quantified using ImageJ software (NIH) on a minimum of six images of cerebral blood vessels per sample.
To estimate expression levels in RNA deep sequencing data, the number of reads that overlapped with exons from known transcripts (as described in Gencode version 14 [ 14]) by no less than 30% of the read's length were quantified using the IntersectBed tool from the BEDTools suite [ 35].
Serotonergic fiber length was quantified using the Isotropic Virtual Planes (IVP) probe of StereoInvestigator [33].
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