Inconsistency in MCNS type level data: Missing neurotransmitter predictions

[floesche]

In MCNS, the following bodyIds don't have a consensusNt assigned, although the majority of their same type does have a consensusNt:

• 43034 (MeTu1). Instead: consensusNt="acetylcholine", celltypePredictedNtConfidence=0.9382293224334717 ?
• 120344 (T2a) Instead: consensusNt="acetylcholine", celltypePredictedNtConfidence=0.0.9536635279655457 ?
• 255964, 301305, 321241, 377394, 415959, 439338, 453447, 954304, 102730610, 102829180, 165307335, 182055376, 187467801, 190960183, 229159256, 237125523, 267864463, 325721459, 345369828, 387136270, 407382048, 482981517, 528648152, 608346676, 635361007, 675422459, 710268570, 785169039, 852693854, 865642428, 871118340, 893816063, 933869224, 999210425 (JO-C/D/E). Instead: consensusNt="acetylcholine", celltypePredictedNtConfidence=0.8536478877067566 ?
• 214264, 953758, 191222213, 225531498, 289189116, 428888752, 433689529, 545758258, 550485938, 595981074, 634015490, 665341618, 696659928, 698835546, 939224751, 963561242, 1001037799, 1018999243 (JO-A): Instead: consensusNt="acetylcholine", celltypePredictedNtConfidence=0.8869533538818359
• 210305, 378122, 138093763, 445096818, 986835763, 1026240572 (JO-B). Instead: consensusNt="acetylcholine", celltypePredictedNtConfidence=0.9059184789657593

[floesche]

@stuarteberg, I just checked. This still seems to be an issue in male-cns:v0.9.

I checked on the neuprint-cns.janelia.org server, assuming the dataset is the same as on neuprint.janelia.org

The other two inconsistency issues were resolved.

[stuarteberg]

Nice find! I notice that none of those cells have any synapses at all:

Details

In [14]: neurons = fetch_neurons([43034, 120344, 255964, 301305, 321241, 377394, 415959, 439338, 453447, 954304, 102730610, 102829180, 165307335, 182055376, 187467801, 190960183, 229159256, 237125523, 26786
    ...: 4463, 325721459, 345369828, 387136270, 407382048, 482981517, 528648152, 608346676, 635361007, 675422459, 710268570, 785169039, 852693854, 865642428, 871118340, 893816063, 933869224, 999210425, 2142
    ...: 64, 953758, 191222213, 225531498, 289189116, 428888752, 433689529, 545758258, 550485938, 595981074, 634015490, 665341618, 696659928, 698835546, 939224751, 963561242, 1001037799, 1018999243, 210305,
    ...:  378122, 138093763, 445096818, 986835763, 1026240572], omit_rois=True)
    ...: _df = neurons[['bodyId', 'type', 'pre', 'post', 'predictedNt', 'predictedNtConfidence', 'consensusNt', 'celltypePredictedNt', 'celltypePredictedNtConfidence']]
    ...: _df
Out[14]:
        bodyId      type  pre  post predictedNt predictedNtConfidence consensusNt celltypePredictedNt celltypePredictedNtConfidence
0        43034     MeTu1    0     0        None                  None        None                None                          None
1       120344       T2a    0     0        None                  None        None                None                          None
2       210305      JO-B    0     0        None                  None        None                None                          None
3       214264      JO-A    0     0        None                  None        None                None                          None
4       255964  JO-C/D/E    0     0        None                  None        None                None                          None
5       301305  JO-C/D/E    0     0        None                  None        None                None                          None
6       321241  JO-C/D/E    0     0        None                  None        None                None                          None
7       377394  JO-C/D/E    0     0        None                  None        None                None                          None
8       378122      JO-B    0     0        None                  None        None                None                          None
9       415959  JO-C/D/E    0     0        None                  None        None                None                          None
10      439338  JO-C/D/E    0     0        None                  None        None                None                          None
11      453447  JO-C/D/E    0     0        None                  None        None                None                          None
12      953758      JO-A    0     0        None                  None        None                None                          None
13      954304  JO-C/D/E    0     0        None                  None        None                None                          None
14   102730610  JO-C/D/E    0     0        None                  None        None                None                          None
15   102829180  JO-C/D/E    0     0        None                  None        None                None                          None
16   138093763      JO-B    0     0        None                  None        None                None                          None
17   165307335  JO-C/D/E    0     0        None                  None        None                None                          None
18   182055376  JO-C/D/E    0     0        None                  None        None                None                          None
19   187467801  JO-C/D/E    0     0        None                  None        None                None                          None
20   190960183  JO-C/D/E    0     0        None                  None        None                None                          None
21   191222213      JO-A    0     0        None                  None        None                None                          None
22   225531498      JO-A    0     0        None                  None        None                None                          None
23   229159256  JO-C/D/E    0     0        None                  None        None                None                          None
24   237125523  JO-C/D/E    0     0        None                  None        None                None                          None
25   267864463  JO-C/D/E    0     0        None                  None        None                None                          None
26   289189116      JO-A    0     0        None                  None        None                None                          None
27   325721459  JO-C/D/E    0     0        None                  None        None                None                          None
28   345369828  JO-C/D/E    0     0        None                  None        None                None                          None
29   387136270  JO-C/D/E    0     0        None                  None        None                None                          None
30   407382048  JO-C/D/E    0     0        None                  None        None                None                          None
31   428888752      JO-A    0     0        None                  None        None                None                          None
32   433689529      JO-A    0     0        None                  None        None                None                          None
33   445096818      JO-B    0     0        None                  None        None                None                          None
34   482981517  JO-C/D/E    0     0        None                  None        None                None                          None
35   528648152  JO-C/D/E    0     0        None                  None        None                None                          None
36   545758258      JO-A    0     0        None                  None        None                None                          None
37   550485938      JO-A    0     0        None                  None        None                None                          None
38   595981074      JO-A    0     0        None                  None        None                None                          None
39   608346676  JO-C/D/E    0     0        None                  None        None                None                          None
40   634015490      JO-A    0     0        None                  None        None                None                          None
41   635361007  JO-C/D/E    0     0        None                  None        None                None                          None
42   665341618      JO-A    0     0        None                  None        None                None                          None
43   675422459  JO-C/D/E    0     0        None                  None        None                None                          None
44   696659928      JO-A    0     0        None                  None        None                None                          None
45   698835546      JO-A    0     0        None                  None        None                None                          None
46   710268570  JO-C/D/E    0     0        None                  None        None                None                          None
47   785169039  JO-C/D/E    0     0        None                  None        None                None                          None
48   852693854  JO-C/D/E    0     0        None                  None        None                None                          None
49   865642428  JO-C/D/E    0     0        None                  None        None                None                          None
50   871118340  JO-C/D/E    0     0        None                  None        None                None                          None
51   893816063  JO-C/D/E    0     0        None                  None        None                None                          None
52   933869224  JO-C/D/E    0     0        None                  None        None                None                          None
53   939224751      JO-A    0     0        None                  None        None                None                          None
54   963561242      JO-A    0     0        None                  None        None                None                          None
55   986835763      JO-B    0     0        None                  None        None                None                          None
56   999210425  JO-C/D/E    0     0        None                  None        None                None                          None
57  1001037799      JO-A    0     0        None                  None        None                None                          None
58  1018999243      JO-A    0     0        None                  None        None                None                          None
59  1026240572      JO-B    0     0        None                  None        None                None                          None

The first two likely had their cell types prematurely backported from the master branch. They are just bare cell bodies, but I would guess that they are actually merged in our master branch to properly typed neurons. (I may try to fix this before the public release, but anyway it will resolve itself in the v1.0 release.)

The others all appear to be sensory neurons which seemingly have no synapses (at least none that our synapse predictor found).

In any case, it is probably not correct that these should be excluded entirely from having a consensusNt. Presumably it's an artifact of how the data is processed. I hadn't considered how it would behave for synapseless neurons.

I will likely not be able to alter the behavior in time for our release, though, unless this is a big problem for your site.

[floesche]

Interesting.

And no, its not a problem for our site