ELM Landmarks created by Bock & Saalfeld groups at Janelia

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)
#>   Label  Use        X         Y        Z       X1        Y1     Z1
#> 1  Pt-1 TRUE 571.4001  38.85996 287.0595 452638.6  93129.93  92560
#> 2  Pt-2 TRUE 715.8113 213.29936 217.3935 522271.2 184057.51  96160
#> 3  Pt-3 TRUE 513.0022 198.00197 217.7941 428701.7 173888.16 112440
#> 4  Pt-6 TRUE 867.0125  31.91925 276.2234 597973.7  99741.26  77200
#> 5  Pt-7 TRUE 935.2109 234.22952 351.5181 629661.1 172401.93 146120
#> 6  Pt-8 TRUE 935.2109 232.62607 405.5008 629608.0 170950.13 185640

if (FALSE) {
# 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)
}