As well as development versions available from GitHub through the previous links, stable versions are periodically released to CRAN (nat and nat.templatebrains). These can be installed in an interactive R session via the following commands:
install.packages('nat') # install devtools package if you don't already have it if (!require("devtools")) install.packages("devtools") # nb this will install the generic templatebrains package from CRAN devtools::install_github("jefferislab/nat.flybrains") # to install additional/updated registrations # (beyond those distributed as part of the R package) # Strongly recommended! nat.flybrains::download_jefferislab_registrations()
Bridging and mirroring example
Below, we briefly show how our R packages can be used to bridge a FlyCircuit neuron in FCWB space into JFRC2 space, followed by a mirroring. To follow along, simply copy and paste the code below into an interactive R session.
library(nat) library(nat.flybrains) # Load a neuron neuron_to_bridge <- kcs20[] # Display the neuron in 3D nopen3d() plot3d(neuron_to_bridge) # Add the original brain to the 3D display, for context plot3d(FCWB)
# Bridge the FCWB neuron into JFRC2 space neuron_in_jfrc2 <- xform_brain(neuron_to_bridge, FCWB, JFRC2) # Plot the bridged neuron in 3D, along with the JFRC2 brain nopen3d() plot3d(neuron_in_jfrc2) plot3d(JFRC2)
# Note that the relative position of the neuron in each brain is the same # Mirror the neuron in JFRC2 neuron_in_jfrc2_mirrored <- mirror_brain(neuron_in_jfrc2, JFRC2) # Plot mirrored neuron in 3D plot3d(neuron_in_jfrc2_mirrored)