write.hdf5: plot merged channel stored in AR?

[mabar1]

Hi all
I was digging in the write.hdf5 function to optimize my merged channel signal. Since many of these channel intensities are skewed beyond repair, I gave a z-score normalization appoach a try, and it turned out quite ok (we dont have memebrane markers in the panel, so I try my best to find a good marker combination).
I am doing similar things like the default function with the min-max normalized channels: clipping the z-scores channel-wise (within the rw.tbl loop), as well as the merged signal intensities in rw.sms.

This approach works nicely in my ROIs, but the thing I struggle is the following: In order to check parameter combinations, I have to export the hdf5 crops and load them into ilastik.... I would like to have an option where the write.hdf5 with plot=T
takes the AR array, actually I just need the Merged channel in there, and plot this channel.
That would allow to run a bunch of different paramters against each other and then just have a look at the merged channel. How do I access the data in AR so that I can plot the merged channel?
Sorry for such a detailed request...
Best matthias

[tomashhurst]

@mabar1 there is actually an argument in the write.hdf5 function that will allow you to create a merged channel, using whichever combination of channels you like.

           channels = for.ilastik,
           merge.channels = merge.channels,
           plots = FALSE)