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The number of spiral and vestibular ganglia neurons within the counting areas was estimated using the stereology-optical disector technique and compared with estimates obtained using the assumption-based Abercrombie method on the same specimens.
Neurons were counted only when the nucleus was in clear focus within the counting frame.
Only Islet-stained nuclei within the counting frame and no contact with exclusion lines were counted using a 40× objective.
The counting frame displayed inclusion and exclusion lines and only immunoreactive cell bodies falling within the counting frame with no contact with the exclusion lines were counted.
Our criterion for counting and measuring the area of an individual TH+ neuron was the presence of its nucleus either within the counting frame, or touching the right or top frame lines (green), but not touching the left or bottom lines (red).
Guard volumes (4 µm from thetop and 4.6 µm from the bottom of the section) were excluded from both surfaces to avoid the problem of lost caps, and only the profiles that came into focus within the counting volume (witha depth of 10 µm) were counted.
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For the measurements in CBA mode, both isotopes intensities are within the linear counting regime of the detector, thus correct values of the isotope fractions can be expected.
Within these counting frames, the number of gold particles associated with plasma membranes, N g, and the number of test points hitting cell profiles, Σ Pcell2, were counted.
Numbers within the circles count upwards with the duration of the touch.
Files produced by featureCounts, including both outputs and summary reports, are available from the project repository in the "data" subfolder within the "Counts" directory.
Expression values in reads per million (RPM) and reads per kilobase transcript per million (RPKM) were calculated for the sm and pm data sets and are also available in the "results" subfolder within the "Counts" directory.
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