Add an example of visualising CMTK registrations

[jefferis]

No description provided.

[young24]

Hello Dr. Jefferis. I'm a PhD student from Felsenberg Lab at FMI. In your previous image registration script, the links in the Data setup section are not valid. Can you help me get these sample data? I'm now trying to use your Natverse and other packages to do some fly brain image registration. I really like these packages they made. Thank you.

[jefferis]

Dear @young24, thanks for your interest in the natverse. The script in question is not really part of the nat.examples package (where all the scripts should run well in isolation) but captures the state of the analysis for a paper.

You should be able to replace the whole Data setup section with this. @jdmanton used specific paths on his local machine (like options(flycircuit.datadir = '~/projects/ChiangReanalysis/data/')) to avoid redownloading stuff but you don't need to.

message("Loading dps...")
dps <- load_fcdata('dpscanon')
options(nat.default.neuronlist = 'dps')
options(rgl.antialias = TRUE)

[young24]

Dear @jefferis , thank you for your response. I tried your code to load the data. However, No brain showed up after I ran the par3d command, which is different from the picture in the script. Is that because the rds data was not loaded into the global environment?

[jefferis]

Hi Wenbin, which code did you try to run? par3d only sets features of the view (zoom, perspective etc), but doesn't plot anything itself. Are you trying to run these sections showing points before and after registration?

clear3d()
points3d(fcwb_orig, col='red', size=12)
points3d(fcwb_affine, col='cyan', size=12)
x <- c(0, 564.25)
y <- c(0, 326)
z <- matrix(c(60, 60, 60, 60), nrow=2)
persp3d(x,y,z, col='white', specular='black', texture='stack_slices/FCWBslice60.png', xlab='', ylab='', zlab='', box=F, axes=F, add=T)
par3d('userMatrix'=structure(c(1, 0, 0, 0, 0, -1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1), .Dim = c(4L, 4L)))

In that case you will need to uncompress the attached files to your working directory.

stack_slices.zip

If you are just trying to do a generic 3d plot, you should be able to do something like this and get a surface:

library(natverse)
clear3d()
plot3d(JFRC2)

More generally, I would recommend to come over to https://groups.google.com/forum/#!forum/nat-user and describe what you would like to do and I will try to give some advice that would help.

[young24]

@jefferis thank you for your reply. I managed to show the brain slice. Now, I understand I didn't give the path to slice pictures...
I will go to the Google Group if I have further questions. Thank you again.