mesh - veeninglab/BactMAP GitHub Wiki

The mesh dataframe is the main output of extr-functions used to import segmentation data. It describes the outlines of cells and their dimensions. Each row in the mesh dataframe represents one point of a cell outline of one given cell.

Format

Basic Mesh Structure

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.

Turned Cells

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

Magnification conversion

When indicated when using one of the extr-functions, the cell lengths, coordinates and widths 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

Other variables

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.