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Cells expressing each one or both markers were manually quantified and normalized to the total amount of Hoechst+ nuclei in the field and expressed as the means±S.E.M. Number of cells lacking the expression of both markers was calculated.
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CD4+CD28null T cells were identified by morphologically cell-like structures with co-localized immunostainings of CD3, CD4 and CD244, and were manually quantified in independent analyses performed by two persons.
For quantification of caspase-3 positive cells, the slides were scanned at 40 × magnification and manually quantified in 60 power fields.
Crystal violet solution was then washed off and colonies were manually quantified.
Intravital microscopy of mutant CSΔN and TRAP-VAL sporozoites in conjunction with fluorescently labeled dermal vascular endothelia was performed, and invasion events were manually quantified.
We first manually quantified root system depth (A ) width (B ) and average lateral root angle (C ) in a set of 15 root systems corresponding to different Arabidopsis accessions.
Figure 2D shows the evolution over time of several root traits that can be automatically captured by GLO-RIA (depth, width, area) and others that were manually quantified (primary root growth rate or number of lateral roots per primary root).
To quantify proliferating endothelial cells, tissue sections that were dually stained for VWF and Ki67 nuclear proliferation antigen were manually quantified.
The cells were observed using a fluorescence microscope (Olympus, Shinjuku-ku, Tokyo, Japan), and the γ-H2AX foci were manually quantified in at least three individual fields of ~100 cells.
As described in Material and methods, the speed of elongation was manually quantified from the proximal end of the photobleached region using ImagePro Plus 6.0 software.
To gain further insights into these differences we manually quantified the evolution of AS cell shape changes using three parameters: apical surface area, elongation and membrane content (Figure 5A and for details on analysis see Materials and Methods).
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