NBLAST_search
NBLAST Search fig
Panels for NBLAST Search figure.
## glX
## 6Scale bar panel A
imscalebar(seq(0,1,len=11),col=jet.colors(10),horizontal=F, mar=c(0,0,0,0))
For types of searches:
Panel B: Neuron against neuron
Plot the query neuron fru-M-400121
#op=par3d(no.readonly=T)
#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 = 0.609543204307556), .Names = c("FOV", "userMatrix",
"scale", "zoom"))
par3d(op)
plot3d("FruMARCM-M001189_seg001", col='black', lwd=3, soma=T)
Use a remote score matrix restricted to auditory neurons
auditory_neurons_score_mat <- load_si_data("auditory_neurons_score_mat.rds")
options(flycircuit.scoremat="auditory_neurons_score_mat")Plot the query and the top hit.
clear3d()
par3d(op)
plot3d("FruMARCM-M001189_seg001", col='black', lwd=3, soma=T)
plot3d(names(sort(fc_nblast("FruMARCM-M001189_seg001"), decreasing=T)[2]), col='red', lwd=3, soma=T)
Plot the top 8.
clear3d()
par3d(op)
plot3d("FruMARCM-M001189_seg001", col='black', lwd=3, soma=T)
plot3d(names(sort(fc_nblast("FruMARCM-M001189_seg001"), decreasing=T)[2]), col='red', lwd=3, soma=T)
plot3d(names(sort(fc_nblast("FruMARCM-M001189_seg001"), decreasing=T)[3:11]), soma=T)
For C panels: neuron segment against whole neurons
Using PNs: isolate medial and outer tract.
For the medial tract: choose one neuron and select tract.
malt1=fc_gene_name(subset(annotation, annotation_class=="MainTract" & text=="mALT")$neuron_idid[1])
clear3d()
op=structure(list(FOV = 0, userMatrix = structure(c(0.702212810516357,
-0.350920796394348, 0.619476675987244, 0, -0.177913621068001,
-0.928978025913239, -0.324571371078491, 0, 0.689379036426544,
0.117704831063747, -0.714773893356323, 0, 0, 0, 0, 1), .Dim = c(4L,
4L)), scale = c(1, 1, 1), zoom = 0.694574952125549), .Names = c("FOV",
"userMatrix", "scale", "zoom"))
par3d(op)
plot3d(malt1, lwd=3, soma=T, col='black')
#s3d=select3d()
#malt1tract=subset(dps[[malt1]], s3d)
#save(malt1tract, file="/GD/LMBD/Papers/2012NBlast/R/malt1tract.rda")Plot neuron and selected tract.
load(file="../../R/malt1tract.rda")
clear3d()
par3d(op)
plot3d(malt1tract, col='red', lwd=5)
plot3d("ChaMARCM-F001159_seg001", lwd=3, soma=T, col='black')
Load some neurons to blast. Typically we would use all the neurons in the database, but to save time for these figures, we restrict to ~800 olfactory PNs.
# all neurons
# dpscanon=read.neurons(dps)
# instead select PNs
pnids=subset(annotation, annotation_class=="NeuronSubType" )$neuron_idid
dpscanon=subset(dps,idid %in% pnids)Blast tract against dps and plot top 10 hits.
sc_malt=nblast(malt1tract, dpscanon)
clear3d()
par3d(op)
plot3d(malt1tract, col='red', lwd=3)
plot3d(names(sort(sc_malt, decreasing=T)[1:10]), soma=T, lwd=3)
Plot only the tract for the top 10 hits.
clear3d()
par3d(op)
plot3d(malt1tract, col='red', lwd=3)
malttop10=dps[names(sort(sc_malt, decreasing=T))[1:10]]
plot3d(prune(malttop10, malt1tract, maxdist=5), lwd=3)
For the outer tract: Select one neuron and select the tract.
oalt1=names(dps[which(fc_glom(names(dps))=="V")])
plot3d("GadMARCM-F000307_seg001", soma=T, col='black')
#oact=select3d()
#oact.vpn=subset(dps[["GadMARCM-F000307_seg001"]],oact)
#save(oact.vpn, file="../../R/oact.vpn.rda")Plot the tract and the neuron.
load(file="../../R/oact.vpn.rda")
oalt1=names(dps[which(fc_glom(names(dps))=="V")])
fc_neuron(oalt1)## [1] "Gad1-F-200095"clear3d()
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 = 0.600000023841858), .Names = c("FOV", "userMatrix",
"scale", "zoom"))
par3d(op)
plot3d(oact.vpn, col='red', lwd=5)
plot3d(oalt1, lwd=3, soma=T, col='black')
Blast tract against dps and plot top 10 hits.
sc_oalt=nblast(oact.vpn, dpscanon)
clear3d()
par3d(op)
plot3d(oact.vpn, col='red', lwd=3)
plot3d(names(sort(sc_oalt, decreasing=T)[1:10]), soma=T, lwd=3)
Plot only the tract for the top 10 hits.
clear3d()
par3d(op)
par3d(zoom=0.7657688)
plot3d(oact.vpn, col='red', lwd=3)
oalttop10=dps[names(sort(sc_oalt, decreasing=T))[1:10]]
plot3d(prune(oalttop10, oact.vpn, maxdist=5), lwd=3)
Panel D: tracing from pMP-e
dpscanon=read.neurons(dps)## Warning in read.neurons(dps): There are 4760 missing neurons!Convert stalk to dotprops and plot.
p1stalk=read.neuron("P1_stalk_skel.am")
p1stalk.fcwb=xform_brain(p1stalk, sample=JFRC2, ref=FCWB)
# convert to dotprops
p1stalk.dps=dotprops(p1stalk.fcwb, resample=1, k=5)
clear3d()
oplat=structure(list(FOV = 0, userMatrix = structure(c(-0.0198177099227905,
0.100070603191853, 0.994782984256744, 0, -0.2661412358284, -0.959607124328613,
0.0912300795316696, 0, 0.963730275630951, -0.262944787740707,
0.0456501543521881, 0, 0, 0, 0, 1), .Dim = c(4L, 4L)), scale = c(1,
1, 1), zoom = 0.9307966), .Names = c("FOV", "userMatrix",
"scale", "zoom"))
par3d(oplat)
plot3d(p1stalk.dps, lwd=3, col='purple')
Blast stalk against all neurons. Plot 10 top hits
# using alpha value weighting to emphasise neurites ...
p1stalk.sca=nblast(p1stalk.dps, dpscanon, UseAlpha = T, normalised = T)
clear3d()
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 = 0.60), .Names = c("FOV", "userMatrix",
"scale", "zoom"))
par3d(op)
plot3d(p1stalk.dps, col='purple', lwd=3)
p1stalk.scatop10=dps[names(sort(p1stalk.sca, decreasing=T))[1:10]]
plot3d(p1stalk.scatop10, lwd=3, soma=T)
Plot in lateral view
clear3d()
oplat=structure(list(FOV = 0, userMatrix = structure(c(-0.0231221914291382,
0.0445186011493206, 0.998740911483765, 0, -0.19016632437706,
-0.980964064598083, 0.039323590695858, 0, 0.981479525566101,
-0.189017653465271, 0.0311479568481445, 0, 0, 0, 0, 1), .Dim = c(4L,
4L)), scale = c(1, 1, 1), zoom = 0.600000023841858), .Names = c("FOV",
"userMatrix", "scale", "zoom"))
par3d(oplat)
plot3d(p1stalk.dps, col='purple', lwd=3)
plot3d(p1stalk.scatop10, lwd=3, soma=T)
Panel E: Gal4 tracing against FC neurons
We were looking for a line that had neurons that followed a dorsal tract. This line was found by a VFB query for expression in the PVLP, scanning the results and downloading the registered image.
JFRC2_GMR_18C12_AE_01_05-fA01b_C100226_20100226143229515_02_warp_m0g80c8e1e-1x26r3.nrrd
Using the tracing of a Janelia GAL4 line (R18C12) made in Vaa3D.
The tracing was converted into dotprops, corrected voxel size and transformed to FCWB.
#R18C12=read.neuron("/GD/LMBD/Papers/2012NBlast/R/R18C12_L.am") # original tracing with subtrees stitched together
#R18C12=R18C12*JFRC2$voxdims # making voxel size correct
#write.neuron(R18C12, file="/GD/LMBD/Papers/2012NBlast/R/R18C12_voxdims.am", format='hxlineset', F=T) #resave with new name
#R18C12=read.neuron(f="/GD/LMBD/Papers/2012NBlast/R/R18C12_voxdims.am")
#R18C12.FCWB=xform_brain(R18C12,sample=JFRC2,ref=FCWB) #transform to FCWB
#write.neuron(R18C12.FCWB, file="/GD/LMBD/Papers/2012NBlast/R/R18C12.FCWB.swc", F=T)Plot the tracing.
R18C12.FCWB=read.neuron(f="R18C12.FCWB.swc")
clear3d()
optrace=structure(list(FOV = 0, userMatrix = structure(c(1, 0, 0, 0,
0, -1, 0, 0, 0, 0, -1, 0, 0.89562052488327, 0.0229582022875547,
0, 1), .Dim = c(4L, 4L)), scale = c(1, 1, 1), zoom = 0.665256559848785), .Names = c("FOV",
"userMatrix", "scale", "zoom"))
par3d(optrace)
plot3d(R18C12.FCWB,lwd=3,col='black')
Blast the trace against the FC neurons and plot the top 3 hits
R18C12.fc.sc.norm=nblast(dotprops(R18C12.FCWB,resample=1,k=5), normalised = T,target=dpscanon)
R18C12.fc.sc.norm.top3=dps[names(sort(R18C12.fc.sc.norm,dec=T))[1:3]]
clear3d()
op=structure(list(FOV = 0, userMatrix = structure(c(1, 0, 0, 0,
0, -1, 0, 0, 0, 0, -1, 0, 0.213899674296162, 6.43469228666443,
0, 1), .Dim = c(4L, 4L)), scale = c(1, 1, 1), zoom = 0.600000083446503), .Names = c("FOV",
"userMatrix", "scale", "zoom"))
par3d(op)
plot3d(R18C12.FCWB,lwd=3, col='black')
plot3d(R18C12.fc.sc.norm.top3, lwd=3, soma=T)
Plot the top hits in dorsal view.
clear3d()
opdors=structure(list(FOV = 0, userMatrix = structure(c(0.99937516450882,
0.0329592153429985, 0.0127521678805351, 0, 0.0169835463166237,
-0.13147696852684, -0.99117374420166, 0, -0.0309914499521255,
0.990770936012268, -0.13195475935936, 0, 3.92906141281128, -7.32608795166016,
-55.9301376342773, 1), .Dim = c(4L, 4L)), scale = c(1, 1, 1),
zoom = 0.600000083446503), .Names = c("FOV", "userMatrix",
"scale", "zoom"))
par3d(opdors)
plot3d(R18C12.FCWB,lwd=3,col='black')
plot3d(R18C12.fc.sc.norm.top3, lwd=3, soma=T)
Panel F: search all traces from FC neuron
Load all traces.
hpproj.FCWB.dps.canon=readRDS("../../R/hpproj.FCWB.dps.canon.rds")Search with one of the previous top hits against all traces.
ntoblast=names(R18C12.fc.sc.norm.top3)[3]
tracesc=nblast(query=dps[[ntoblast]], target=hpproj.FCWB.dps.canon, normalised = T)
tracesctop10=names(sort(tracesc, dec=T))[1:10]
clear3d()
par3d(op)
plot3d(ntoblast, lwd=3, soma=T, col='black')
Plot top 10 hits against the neuron (VGlut-F-500818)
clear3d()
par3d(op)
plot3d(ntoblast, lwd=3, soma=T, col='black')
plot3d(tracesctop10, lwd=3, db=hpproj.FCWB.dps.canon)
Plot top 10 hits in dorsal view.
clear3d()
par3d(opdors)
plot3d(ntoblast, lwd=3, soma=T, col='black')
plot3d(tracesctop10, lwd=3, db=hpproj.FCWB.dps.canon)