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Get SWC neuron support in HC in line with new "official" spec #75

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porterbot opened this issue Oct 29, 2024 · 1 comment
Open

Get SWC neuron support in HC in line with new "official" spec #75

porterbot opened this issue Oct 29, 2024 · 1 comment
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@porterbot porterbot converted this from a draft issue Oct 29, 2024
@olbris
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olbris commented Nov 4, 2024

Here's output from their validator on one of our neurons:

2020-09-15_G-010_Consensus.swc
    0   Missing Field Columns   False   PASS    
    1   No. of tree samples 9661    PASS    
    2   No. of soma samples 0   PASS    Warning! No soma samples found.
    3   Root ParentIndex    -1  PASS    
    4   Invalid ParentIndex False   PASS    
    5   NonStandard TypeID  True    FAIL    ERROR: Bifucartions tagged as 5 and Terminals tagged as 6
    6   ITP int True    PASS    
    7   XYZ double  True    PASS    
    8   Radius positive double  True    PASS    
    9   Index sequential    True    PASS    
    10  Sorted Index Order  True    PASS    
    11  Contour False   PASS    Warning! No soma samples found.
    12  Abnormal Compartments   True    PASS    Warning! Abnormal compartments detected with very long lengths.

Our only fail is that we set some types based on geometry (branch, end) which is no longer allowed. Easy to fix.

We may discuss other adjustments while we're in the code. Eg, supporting soma tags, or possibly retiring the OFFSET header.

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