Localization Part 3 - veeninglab/BactMAP GitHub Wiki

We can view the cells & spots by plotting them using plotRaw().

plotRaw() has many input options; we'll go through the basics below using the Staphylococcus aureus dataset as an example. First, we will use it to do basic plotting of the segmentation over the image, then we'll modify the plot.

Try it yourself using the other datasets!

To plot a simple projection, specify the tiffdata, meshdata and/or spotdata. Note that you can also plot only one or two of these three datasets using plotRaw()! Next to the data input, specify which frame of the image stack you want to plot by setting frameN (default = 1).

plotRaw(tiffdata=stack_Staph,
        meshdata=mesh_Staph$mesh,
        spotdata=spots_Staph$spotframe,
        frameN=1)

You can zoom in by changing the x and y-limits of the plot. Do this by setting xrange and yrange to a set of pixels, for instance: xrange = c(200, 600) to show only the pixels on the x axis between 200 and 600.

You can also change the contrast by setting the range of values shown. Do this by setting valuerange to a different number. For this, it is useful to first get an idea of the distribution of your intensity values. The easiest way to achieve this is by setting legend to TRUE in plotRaw():

plotRaw(tiffdata=stack_Staph,
        meshdata=mesh_Staph$mesh,
        spotdata=spots_Staph$spotframe,
        frameN=1,
        legend=TRUE)

Here you see that the image is black, which is in the range of 0-~0.025. Changing the valuerange to 0-0.025 will change the color distribution so we can see the cells better. At the same time, let's change xrange and yrange so we can zoom in:

plotRaw(tiffdata=stack_Staph,
        meshdata=mesh_Staph$mesh,
        spotdata=spots_Staph$spotframe,
        xrange=c(1000,1200),
        yrange=c(500,800),
        valuerange=c(0, 0.025))

To see the fluorescent spots better, you might need to play around with the valuerange a bit more. Try this for the S. aureus image as well as for the other two image stacks!