NBLAST_algorithm

NBLAST figure

Some of the panels for NBLAST_algorithm figure.

Sample 50 neurons before and after flipping (original and flipped, respectively).

set.seed(18)
sample3=sample(dps,50)

Plot 50 flipped neurons.

nopen3d()

## glX 
##   5

plot3d(FCWB)
# op=par3d(no.readonly = F)
# dput(op[par3dmini])
op=structure(list(FOV = 0, userMatrix = structure(c(1, 0, 0, 0, 
0, -1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1), .Dim = c(4L, 4L)), scale = c(1, 
1, 1), zoom = 0.587089359760284), .Names = c("FOV", "userMatrix", 
"scale", "zoom"))
par3d(op)
plot3d(names(sample3), soma=T, col=rainbow(50))

And now the unflipped version.

flipped3=with(sample3, flipped)
sorig3<-mirror_brain(sample3, subset=flipped3, brain = FCWB)
#extract metadata df
df=attr(sorig3,'df')
# mirror the cell body pos for neurons we just flipped
mirrored_cb_pos=mirror_brain(attr(sorig3,'df')[flipped3, c("X", "Y", "Z")], brain=FCWB)
df[rownames(mirrored_cb_pos),colnames(mirrored_cb_pos)]=mirrored_cb_pos
attr(sorig3, 'df')=df
clear3d()
plot3d(FCWB)
par3d(op)
plot3d(sorig3, soma=T)

Nearest neighbour diagram

Plot 2 neurons for nearest neighbour diagram, one in red and one in black.

clear3d()
op=
structure(list(FOV = 0, userMatrix = structure(c(0.991477966308594, 
-0.0432921275496483, 0.122870959341526, 0, -0.0529103018343449, 
-0.995693325996399, 0.076126255095005, 0, 0.119046114385128, 
-0.0819786190986633, -0.989498555660248, 0, -11.4607306188373, 
3.65054376386083, 2.88657986402541e-15, 1), .Dim = c(4L, 4L)), 
    scale = c(1, 1, 1), zoom = 0.822702646255493), .Names = c("FOV", 
"userMatrix", "scale", "zoom"))
par3d(op)
plot3d("FruMARCM-M002099_seg001",col='red',lwd=2, soma=T)
plot3d("FruMARCM-M002609_seg001", lwd=2, soma=T, col='black')

DL2 neurons

Plot the DL2 PNs used to generate the right prob(match).

dl2=subset(glomdf, grepl('DL2', text))$gene_name
dl2=intersect(dl2, good_images)
length(dl2)

## [1] 180

greenpal=rainbow(length(intersect(dl2, good_images)), start=2/6, end=0.49999999, s=c(0.5, 0.6, 0.7, 0.8, 0.9, 1), v=c(0.5, 0.6, 0.7, 0.8, 0.9, 1))
clear3d()
plot3d(FCWB)
op=structure(list(FOV = 0, userMatrix = structure(c(1, 0, 0, 0, 
0, -1, 0, 0, 0, 0, -1, 0, -86.3129562633307, -50.984995041813, 
0, 1), .Dim = c(4L, 4L)), scale = c(1, 1, 1), zoom = 0.246810808777809), .Names = c("FOV", 
"userMatrix", "scale", "zoom"))
par3d(op)
plot3d(dl2, soma=T, col=greenpal)