elmr builds on the nat and catmaid packages to provide tools to read, analyse, plot, transform and convert neuroanatomical data, especially as it relates to whole brain EM voumes generated at the HHMI Janelia Research Campus (groups of Davi Bock, Stephan Saalfeld and many collaborators).
xform_brain
allows you to transform FAFB data into a large number of other template
brain spaces by making use of the nat.templatebrains
and
nat.flybrains
packages. The ability to move beyond the
JFRC2013
template brain depends on having a
functional CMTK installation. See cmtk.bindir
for more
information and advice about installation.
fetchn_fafb
allows you to fetch FAFB catmaid tracings
and transform to a new template.
nblast_fafb
allows you to nblast catmaid tracings
against a set of neuron skeletons e.g. from flycircuit.
open_fafb
allows you to open a catmaid session in your
browser at a specific xyz location based on selecting a position in any
template brain space e.g. a flycircuit.tw neuron or a JFRC2010 registered
GAL4 line.
stitch_neurons
allows neuron fragments to be stitched
together reasonably intelligently.
FAFB13
a
templatebrain
object specifying the
dimensions of the FAFB EM volume.
elm.landmarks
a set of landmarks that can define a thin
plate spline transform mapping FAFB to light level template brains.
Interacting with a catmaid server will normally
require authentication. Please see
https://github.com/jefferis/rcatmaid#Authentication for details of
how to set up authentication. If you regularly use a particular catmaid
server it is recommended to put authentication in your
Rprofile
file.
There is one package option:
elmr.nblast.cores
Set the default number of cores to use for
parallel nblast. You will need to ensure that the doParallel package (a
suggested but not strict dependency of elmr is installed)
You can set these options in your Rprofile
file.
# position of antennal lobe glomeruli "V" in JFRC2013 template brain vgloms.jfrc2013=data.frame(X=c(316,229), Y=c(143, 139), Z=c(26,22), row.names=c("V_L", "V_R")) # Convert to FAFB12 coordinates xform_brain(vgloms.jfrc2013, sample = JFRC2013, reference = FAFB13)#> X Y Z #> V_L 655021.4 371548.0 45612.92 #> V_R 536193.0 359548.5 55372.38# Show state of elmr package options options()[grep('^elmr', names(options()))]#> $elmr.nblast.cores #> [1] 7 #>## Not run: ------------------------------------ # # Conversion of neurons from FlyCircuit template # # NB this conversion depends on a full install of nat.flybrains and CMTK # library(nat) # kcs13.fafb=xform_brain(kcs20[1:3], sample=FCWB, reference=FAFB13) ## ---------------------------------------------