elm.landmarks: ELM Landmarks created by Bock & Saalfeld groups at Janelia

In jefferis/elmr: Support for working with light and electron microscopy fly brain data

ELM Landmarks created by Bock & Saalfeld groups at Janelia

Description

These are used to map locations in EM (FAFB) space to JFRC2013 (aka DPX) space, in conjunction with a thin plate spline library.

elm.landmarks.12 contains the landmark positions used for the FAFB12 assembly as a historical record.

elm.landmarks.13 contains the landmark positions used for the FAFB13 assembly (from March to Sep 2017) as a historical record.

Details

X,Y,Z correspond to locations in JFRC2013 template brain. However, they are in raw voxel coordinates. In contrast, X1,Y1,Z1 (which contain locations in FAFB space) are in nm.

The current iteration of these landmarks are in FAFB13 space

References

See https://github.com/saalfeldlab/elm for the original source of the landmarks.

Examples

head(elm.landmarks)

## Not run: 
# Show landmarks in the context of the JFRC2013 template brain
library(nat.flybrains)
plot3d(JFRC2013)
# note that the landmarks are in raw voxel coordinates and must be scaled
xyz=scale(elm.landmarks[,c("X","Y","Z")], scale = 1/voxdims(JFRC2013), center = FALSE)
spheres3d(xyz, col = ifelse(elm.landmarks$Use, "green", 'red'), radius = 4)

## End(Not run)

jefferis/elmr documentation built on Sept. 9, 2023, 1:54 p.m.