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Each result was corrected by subtraction of mean background intensities for each channel.
Scanned images were analyzed by Feature Extraction 9.5.3 software (Agilent Technologies), and image analysis and normalization software were employed to quantify the signal and background intensities for each feature.
The scanned images were analyzed by Feature Extraction software 9.5.3 (Agilent Technologies); imaging analysis and a normalization software used to quantify the signal and background intensities for each feature substantially normalized the data by the rank-consistency-filtering LOWESS method.
Images of the arrays were acquired by scanning (Agilent DNA Microarray scanner- Agilent technologies, Palo Alto, USA) and quantification of the signal and background intensities for each spot for the two channels Cy3 and Cy5 was performed by Imagene 5.6 software (Biodiscovery Ltd, Marina del Rey, CA, USA).
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The raw intensity values representing expression of individual transcripts were corrected by subtraction of the background intensity for each array.
Image analysis and normalization software were used to quantify the signal and background intensity for each feature.
Whole-worm GFP intensity was quantified in P sod-3 :: gfp animals using Metamorph (Molecular Devices, Sunnyvale, CA, USA), subtracting local background intensity for each worm.
Agilent Feature Extraction software (version 9.5.3) was used for image analysis, and normalization software was used to quantify the signal and background intensity for each feature.
To evaluate microarray coverage of UHRR, UMRR and URRR on other microarrays, average background intensity values were used as thresholds (either 1X or 2X the background intensity for each channel; Table 3).
The intensity of each projected GFP focus was determined by drawing a ∼150 nm circumference centered in the middle of the focus, subtracting the average background intensity for each field.
Images were acquired and processed as above, and the intensity of the α-Tubulin signal at the KT measured and normalized against the KT CREST signal, after subtraction of cytoplasmic background intensity for each individual cell.
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