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The live, apoptotic, and dead cells in the spheroid outer shell were visualized by optical section using a 20X water immersion objective up to a depth of 100 µm using Hoechst 33342 (live), Yo-Pro-1 (apoptotic), and propidium iodide (dead) (Invitrogen, Grand Island, NY) vital dyes on a Nikon A1R multiphoton microscope with Mai Tai DeepSee tunable IR laser at 750 nm.
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Mitochondrial transport was visualized by time-lapse imaging of a single optical section using only the 543 nm laser, at a frequency of ~1 Hz, for 6 minutes.
Serial 50 µm coronal sections of cerebellum were immunostained and imaged through a 63× (1.3 NA) oil objective by 0.4 µm optical sectioning using a Zeiss 710 confocal microscope (Carl Zeiss Inc., Oberkochen, Germany).
Three-dimensional immunofluorescence images were reconstructed from 0.5 mm confocal optical sections using VOLOCITY 3.6 software (Improvision, Lexington, MA, USA).
Deep-tissue three-dimensional imaging of elastic fibers with submicron spatial resolution was performed by optical sectioning of heart valves using a multiphoton laser scanning microscope in connection with a tunable 80 MHz femtosecond laser source.
Each colony was imaged from bottom to top by optical sectioning in 5 μm steps.
Signals were evaluated by optical sectioning and three-dimensional imaging as previously described [ 15].
The intracellular localization of IGF-II-QD655 complexes was assessed in more detail by optical sectioning.
This ring-like localization pattern was confirmed by analysis of optical sections obtained using confocal microscopy (Figure S3).
Three-dimensional immunofluorescence images were reconstructed from 0.5-µm confocal optical sections by using VOLOCITY 3.6 (Improvision, Lexington, MA).
All sections were semi-quantitatively analyzed by Image Pro Plus (IPP) version 6.0 software, and the integrated optical density (IOD) was measured from staining of six fields for each section, using one section per rat, on the images at 400× magnification.
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