mesh | R Documentation |
When extracting segmentation data, the main output is a dataframe called 'mesh'. The standard structure of this dataframe is shown below:
A data frame with at least the following 7 variables:
X
a numeric vector indicating the X-coordinate of one mesh outline point.
Y
a numeric vector indicating the Y-coordinate of one mesh outline point.
cell
a numeric vector giving the cell ID (unique per image frame)
frame
a numeric vector giving the ID of the image frame
max.length
a numeric vector giving the cell length (in pixels)
max.width
a numeric vector giving the cell diameter (in pixels)
num
a numeric vector indicating the order of the cell outline points.
When the cells are turned (default) such, that the mid-point is at [0,0] and the length axis is parallel to the x axis, the following 5 variables are added:
angle
the angle of the cell length axis towards the 0 x-axis
Xmid
the X-coordinate of the cell's midpoint
Ymid
the Y-coordinate of the cell's midpoint
X_rot
the X-coordinate of the turned cell
Y_rot
the Y-coordinate of the turned cell
When a magnification conversion factor is indicated, the coordinates and lengths are calculated in micron. The following 4 variables are added:
Xrot_micron
the X-coordinate of the turned cell in micron
Yrot_micron
the Y-coordinate of the turned cell in micron
max_um
the cell length in micron
maxwum
the cell width in micron
In most cases, the cell area is also indicated:
area
The cell area in pixel^2
Finally, depending on the input programs, some other variables can be added to the output. See the original programs output documentation for clarification.
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