sanjayankur31
commented
2 months ago In the allen inst cell, the apical dendrites aren't included in the "dendrite_group":
a = cell.get_ordered_segments_in_groups(["all", "soma_group", "dendrite_group", "axon_group", "dend", "apic"])Checking:
In [39]: len(a["apic"]) + len(a["dendrite_group"]) + len(a["soma_group"]) + len(a["axon_group"])
Out[39]: 3489
In [40]: len(a["all"])
Out[40]: 3489
In [41]: len(a["dendrite_group"]) + len(a["soma_group"]) + len(a["axon_group"])
Out[41]: 1161@pgleeson : I guess the apical dendrites segment group apic should also be included in the dendrite_group here?
In the HL23PYR cell, there are 22 segments in the myelin_group that aren't in the conventional groups:
a = cell.get_ordered_segments_in_groups(["all", "soma_group", "dendrite_group", "axon_group", "basal_dendrite_group", "apical_dendrite_group", "myelin_group"])here's verification:
(a["myelin_group"])
Out[12]:
[<Segment|5819|Seg0_myelin_0>,
<Segment|5820|Seg1_myelin_0>,
<Segment|5821|Seg2_myelin_0>,
<Segment|5822|Seg3_myelin_0>,
<Segment|5823|Seg4_myelin_0>,
<Segment|5824|Seg5_myelin_0>,
<Segment|5825|Seg6_myelin_0>,
<Segment|5826|Seg7_myelin_0>,
<Segment|5827|Seg8_myelin_0>,
<Segment|5828|Seg9_myelin_0>,
<Segment|5829|Seg10_myelin_0>,
<Segment|5830|Seg11_myelin_0>,
<Segment|5831|Seg12_myelin_0>,
<Segment|5832|Seg13_myelin_0>,
<Segment|5833|Seg14_myelin_0>,
<Segment|5834|Seg15_myelin_0>,
<Segment|5835|Seg16_myelin_0>,
<Segment|5836|Seg17_myelin_0>,
<Segment|5837|Seg18_myelin_0>,
<Segment|5838|Seg19_myelin_0>,
<Segment|5839|Seg20_myelin_0>,
<Segment|5840|Seg21_myelin_0>]
In [7]: len(a["dendrite_group"]) + len(a["soma_group"]) + len(a["axon_group"])
Out[7]: 5818
In [8]: len(a["myelin_group"])
Out[8]: 22
In [9]: len(a["all"])
Out[9]: 5840I don't think the myelin segments are meant to be in any of the standard groups, so this seems correct?
Using the ExportSWC class to export NeuroML2 to SWC works, but it has some checks that aren't necessarily correct for all cell models.
For example, on valid cells like the HL23PYR cell, it throws this exception:
I need to check why these numbers don't add up---where are the 22 segments? But I also see it with other cells, like this one from the Allen cells: https://github.com/OpenSourceBrain/AllenInstituteNeuroML/blob/master/CellTypesDatabase/models/NeuroML2/Cell_497232312.cell.nml