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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).
Cell characteristics were manually quantified on a population level.
The number of motor neurons on each section was manually quantified in ImageJ.
Crystal violet solution was then washed off and colonies were manually quantified.
The positive cells were then manually quantified in 10, 40 × power fields from each sample.
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.
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Acquire multiple exposure times to manually quantify every visible metastatic focus.
Of course, manually quantifying what constitutes a 'large' deviation is very hard to do.
We tested the ability of GLO1-generated images to reveal complete root systems by manually quantifying the number of lateral roots in excavated root systems of eight different plants and testing these results against estimates of lateral root number from images of the same plants visually inspected by four different persons.
Protein spots from individual gels of the different ganglia groups were outlined (automatically and manually) and quantified using the Proteomweaver (Definiens, Munich, Germany) as previously described.
The LV myocardium and the MI area were manually contoured and quantified.
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