Pixels2um

Add and look up magnification factor “pixels2um”

Description

Functions to check the pixel to micron conversion factors loaded into bactMAP and to add new conversion factors. The new conversion factors will be saved throughout the running R session.

Usage

getPixels2um()

addPixels2um(pixelName, pixels2um)

Arguments

• pixelName A character string identifying your new conversion factor

• pixels2um A numerical value to convert the pixel values to microns

Value

addPixels2um() adds the pixel conversion factor to the list of pixel conversion factors. For the rest of the R session, you can use your given pixelName to call the pixel conversion factor in BactMAP functions.

getPixels2um() and addPixels2um(pixelName, pixels2um) both return the currently loaded conversion factors as a list of vectors, where the first item of each vector is the conversionfactor-name and the second item is the numeric conversion factor.

Note

If you don’t know your pixel conversion factor, open your original images in FIJI/ImageJ and check the Properties of the image.

Author(s)

Renske van Raaphorst

Examples

## To check the currently loaded pixel conversion factors:
getPixels2um()

## To add your pixel conversion factor to bactMAP:
addPixels2um("MyPixel2um", 0.543)