cell questions

[tgbugs]

Questions inspired by hbp_cell_ontology classes

Is there a curation manual for these classifications?

Issues with Thick vs Thin -> Thick vs Narrow/Slender. Is there a different between narrow and slender?

HBP_CELL:0000024 rdf:type owl:Class ;
                  rdfs:label "Untufted pyramidal cell"@en ;
                  nsu:definition "These cells have a thin apical dendrite without a tuft. The two types of Thick Tufted pyramidal cells have bigger and more typical pyramidal-shaped somata compared with Untufted
(slender) pyramidal cells and the Untufted pyramidal cells. The Untufted (slender) pyramidal cells and
the Untufted pyramidal cells are smaller neurons which have similar smaller basal dendritic
clusters."@en ;
                  nsu:synonym "UTPC"@en ;

HBP_CELL:0000041 rdf:type owl:Class ;
                  rdfs:label "Untufted slender pyramidal cell"@en ;
                  nsu:synonym "USPC"@en ;

HBP_CELL:0000032 rdf:type owl:Class ;
                  rdfs:label "Narrow pyramidal cell projecting to thalamus"@en ;
                  nsu:definition "Narrow pyramidal cells have a narrow-looking appearance with short
basal and oblique dendrites and a small tuft."@en ;
                  nsu:synonym "NPC"@en ;

HBP_CELL:0000038 rdf:type owl:Class ;
                  rdfs:label "Slender tufted pyramidal cell"@en ;
                  nsu:definition "These cells have a thin apical dendrite with a small tuft."@en ;
                  nsu:synonym "STPC"@en ;

Are horizontal pyramidal cells actually horizontal tufted pyramidal cells? Similarly are biopolar pyramidal cells actually biopolar untufted pyramidal cells?

HBP_CELL:0000030 rdf:type owl:Class ;
                  rdfs:label "Horizontal pyramidal cell"@en ;
                  nsu:definition "Horizontal tufted pyramidal cells have a horizontally extended dendrite
with more branches than a typical basal dendrite."@en ;
                  nsu:synonym "HPC"@en ;

HBP_CELL:0000031 rdf:type owl:Class ;
                  rdfs:label "Bipolar pyramidal cell"@en ;
                  nsu:definition "Bipolar pyramidal cells have a typical apical dendrite towards pial with
or without a small tuft and a big inverted (towards white matter) dendrite with more branches than
other basal dendrites."@en ;
                  nsu:synonym "BPC"@en ;

Include untufted and slender in the bag for star?

HBP_CELL:0000027 rdf:type owl:Class ;
                  rdfs:label "Star pyramidal cell"@en ;
                  nsu:definition "Star pyramidal cells have a slender apical dendrite without a tuft."@en ;
                  nsu:synonym "SP"@en ;
                  nsu:synonym "SPC"@en ;

Relevant excerpts from p3 of the suplement to https://doi.org/10.1016/j.cell.2015.09.029. Question arrising from these excerpts: are all L4_PC neurons actually L4_TPC neurons? Were narrow and slender substituted for thin as suggested by this text from the suplement?

Layer 4 PCs: There were 3 excitatory m-types in layer 4 (Feldmeyer et al., 1999): 1) L4PC (tufted PC) had an
apical dendrite with a small tuft that often did not extend to layer 1. 2) L4SP (untufted PC, or Star PC) had a
slender apical dendrite without a tuft. 3) L4SS (Spiny Stellate cell) had an apical dendrite with one or few
branches, having a radial length similar to basal dendrites. In comparison with the L4PC and L4SP m-types,
L4SS had tortuous and thicker basal dendritic segments.

Layer 5 PCs: There were 4 PC m-types in layer 5 (Frick et al., 2007; Kasper et al., 1994; Markram et al.,
1997; Romand et al., 2011): 1) L5TTPC1 (Thick-tufted PC 1) had a thick apical dendrite with a big tuft that
bifurcated at the distal half of the apical dendrite. 2) L5TTPC2 (Thick-tufted PC 2) had a thick apical trunk that
bifurcated at the proximal half of the apical dendrite into multiple apical dendrites that further bifurcated
respectively forming a smaller tuft in layer I. 3) L5STPC (small tufted PC) had a thin apical dendrite with a
small tuft. 4) L5UTPC (untufted PC) had a thin apical dendrite without a tuft. The L5TTPCs had bigger and
more typical pyramidal-shaped somata compared to L5STPC and L5UTPC. While L5TTPC1 and L5TTPC2
were bigger neurons with basal dendritic clusters, L5STPC and the L5UTPC were smaller with similar basal
dendritic clusters.

Layer 6 PCs: There were 5 PC m-types layer 6: 1) L6TPC (Tufted PC) had an apical dendrite with a tuft
terminating in either layer 1 or 4. 2) L6UTPC (untufted PC) had an apical dendrite without a tuft. 3) L6IPC
(Inverted PC) had large dendrites inverted towards the white matter with more branches than other basal
dendrites. 4) L6BPC (Bipolar PC) had a typical apical dendrite towards the pia with or without a small tuft and
a big inverted dendrite (towards the white matter) with more branches than other basal dendrites. According to
retrograde labeling experiments, L6BPCs were similar to cortico-claustral PCs projecting to the ipsilateral
claustrum; L6TPCs, L6UTPCs, and L6IPCs corresponded to cortico-cortical PCs projecting to the contralateral
somatosensory cortex (also see (Kisvárday et al., 1990)).

[tgbugs]

@MFSY @srjimenez Here are my initial questions about cell types.

[tgbugs]

Follow up question. Are L5STPCs small-tufted or slender tufted? I haven't seen the small-tufted version of this in the m-types before.