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Bright punctate EEA1 or LAMP1 staining areas with a diameter of 3 microns or less were automatically counted using the spot count feature for EEA1+LAMP1 +CypHer+ and EEA1+LAMP1+CypHer- cells.
Spines were automatically counted using Image-Pro software.
CFUs were automatically counted using OpenCFU (Geissmann 2013).
The percentage of fluorescent VGAT or VGLUT1 puncta was automatically counted using the MetaMorph Count Nuclei application module (Molecular Devices).
Markings in these images were automatically counted using the Photoshop plug-in FoveaPro 4 (Reindeer Graphics, Asheville, USA).
The number of spots, indicating an antigen-specific CTL response, was automatically counted using the Eliphoto system (Minerva Tech, Tokyo, Japan).
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Counting of BrdU-positive cells was performed automatically, using Volocity software (PerkinElmer Inc., Waltham, MA, USA), and manually counted using Image J software.
The number of pixels of each class of causal factors were automatically counted by using the reclassify tool in ArcGIS software and the number pixels of landslide occurrence in each class of causal factors was found on overlaying them.
Biotinylated anti-IFN-γ mAb (XMG1.2), alkaline phosphatase-conjugated streptavidin (PharMingen, Le Pont de Claix, France) and 5-Bromo-5-Chloro-3-Indolyl Phosphate/Nitro"Blue" Tetrazolium (Sigma), as phosphatase substrate, were used to reveal the spots, automatically counted by use of a Bioreader-3000 Pro (BIO-SYS, Karben, Germany).
The number of Fos+ and Fos-GAD plotted neurons per structure was automatically counted and exported using Mercator (ExploraNova).
For the detection of proliferation rates, cardiac fibroblasts (passage 2) were trypsinized and automatically counted in suspension using a Cellometer Auto T4 (Nexcelom Bioscience, Lawrence, MA).
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