Mesh: Format of the Mesh dataframe
In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data
mesh R Documentation
Format of the Mesh dataframe
Description
When extracting segmentation data, the main output is a dataframe called 'mesh'. The standard structure of this dataframe is shown below:
Format
A data frame with at least the following 7 variables:
Xa numeric vector indicating the X-coordinate of one mesh outline point.
Ya numeric vector indicating the Y-coordinate of one mesh outline point.
cella numeric vector giving the cell ID (unique per image frame)
framea numeric vector giving the ID of the image frame
max.lengtha numeric vector giving the cell length (in pixels)
max.widtha numeric vector giving the cell diameter (in pixels)
numa 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:
anglethe angle of the cell length axis towards the 0 x-axis
Xmidthe X-coordinate of the cell's midpoint
Ymidthe Y-coordinate of the cell's midpoint
X_rotthe X-coordinate of the turned cell
Y_rotthe 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_micronthe X-coordinate of the turned cell in micron
Yrot_micronthe Y-coordinate of the turned cell in micron
max_umthe cell length in micron
maxwumthe cell width in micron
In most cases, the cell area is also indicated:
areaThe 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.
vrrenske/shinyspots documentation built on Oct. 28, 2023, 12:26 p.m.
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| mesh | R Documentation |
Format of the Mesh dataframe
Description
When extracting segmentation data, the main output is a dataframe called 'mesh'. The standard structure of this dataframe is shown below:
Format
A data frame with at least the following 7 variables:
Xa numeric vector indicating the X-coordinate of one mesh outline point.
Ya numeric vector indicating the Y-coordinate of one mesh outline point.
cella numeric vector giving the cell ID (unique per image frame)
framea numeric vector giving the ID of the image frame
max.lengtha numeric vector giving the cell length (in pixels)
max.widtha numeric vector giving the cell diameter (in pixels)
numa 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:
anglethe angle of the cell length axis towards the 0 x-axis
Xmidthe X-coordinate of the cell's midpoint
Ymidthe Y-coordinate of the cell's midpoint
X_rotthe X-coordinate of the turned cell
Y_rotthe 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_micronthe X-coordinate of the turned cell in micron
Yrot_micronthe Y-coordinate of the turned cell in micron
max_umthe cell length in micron
maxwumthe cell width in micron
In most cases, the cell area is also indicated:
areaThe 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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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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