glom=="VAsomething" in allpndps.rds is VA4?

[zhihaozheng]

I wrote a short script, which NBLASTed 2 Flycircuit PNs (glom=="VAsomething") against FAFB PNs of VAs glomeruli, to see which VA glomerulus they are from. You should be able to just run the script and it will print the result.

Looks like they are VA4. When plotted, they look like VA4 as well.

[jefferis]

Thanks, @zhihaozheng. When we were annotating the flycircuit neurons, @mmc46 and I had a lot of trouble with a couple of glomeruli in that ares (it also happened that the specimens were not very good).

> grep("VA[4s]", fc_glom(), value = T)
     DvGlutMARCM-F078_seg1     DvGlutMARCM-F1323_seg3 DvGlutMARCM-F004044_seg001 DvGlutMARCM-F003970_seg001 
             "VAsomething"              "VAsomething"                      "VA4"                      "VA4" 
DvGlutMARCM-F003905_seg001 DvGlutMARCM-F002307_seg001 
                     "VA4"                      "VA4" 

Although we settled on VA4 for one class, we could not then assign the other, resulting in VAsomething. When looking at the EM data last summer, we concluded that we must have been wrong in our flycircuit annotations. You should be able to see our notes here if logged in.

Now Marta, I don't remember if we had a firm conclusion about the best alternate for the flycircuit VA4s.

[mmc46]

We thought they could be VA3s, our initial guess.

…

On 2 Feb 2017, at 12:37, Gregory Jefferis ***@***.***> wrote: Thanks, @zhihaozheng <https://github.com/zhihaozheng>. When we were annotating the flycircuit neurons, @mmc46 <https://github.com/mmc46> and I had a lot of trouble with a couple of glomeruli in that ares (it also happened that the specimens were not very good). > grep("VA[4s]", fc_glom(), value = T) DvGlutMARCM-F078_seg1 DvGlutMARCM-F1323_seg3 DvGlutMARCM-F004044_seg001 DvGlutMARCM-F003970_seg001 "VAsomething" "VAsomething" "VA4" "VA4" DvGlutMARCM-F003905_seg001 DvGlutMARCM-F002307_seg001 "VA4" "VA4" Although we settled on VA4 for one class, we could not then assign the other, resulting in VAsomething. When looking at the EM data last summer, we concluded that we must have been wrong in our flycircuit annotations. You should be able to see our notes here <https://github.com/flyconnectome/summer2016/blob/master/pns/PNsMetaData.csv> if logged in. Now Marta, I don't remember if we had a firm conclusion about the best alternate for the flycircuit VA4s. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#42 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AByQ0yI_g8diQbWRO6TdH8jIr5K3NciNks5rYc4NgaJpZM4L0tyX>.

[mmc46]

I've had another look at the registered images for these VAsomething neurons. The position of the glomerulus is anterior and dorsal to the annotated VA4 ones (used DvGlutMARCM-F004044_seg001), so it would match VA3. But it doesn't match VA3 for lineage (or LH arbour so much, looking at the 2 VA3's in CATMAID).
And the glom position doesn't match any other glom nearby.

I'll need to look at the unregistered images, to see what distortion there might be.

[jefferis]

Thanks for rechecking @mmc46. VA3 is pretty recognisable so we can be fairly sure they aren't those as you conclude above. All of this leaves me somewhat concerned that there could be some kind of error propagating from the VC3 area.