The mesh dataframe

The mesh dataframe describes the cell outline and cell dimensions (length, width and if given, area). Each row represents one point of the cell outline of one cell (which one is indicated by the variable "cell"). The mesh dataframe can be used to draw cell outlines, connect spot coordinates to cell information and to draw kymographs in combination with a TIFF of the original microscopy image.

mesh dataframes can be obtained by importing segmentation output using one of the *extr_*functions. See Import Data to find which functions produce mesh dataframes as output.

Format

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.