Specification Neurolucida

Because there is no official Neurolucida specification, this page aims to fill this gap, and provides a subjective specification of the format.

Soma

• Files without a soma are valid.

• Multiple soma ASC files with multiple CellBody tags will raise an error. Unit test

Duplicate points

When reading an ASC file, the last point of a section will be added as the first point of the child sections if not already present. That means these two representations are equivalent:

( (Dendrite)
  (3 -4 0 2)
  (3 -10 0 2)
  (
    (0 -10 0 2)
    (-3 -10 0 2)
  |
    (6 -10 0 2)
    (9 -10 0 2)
  )
)

( (Dendrite)
  (3 -4 0 2)
  (3 -10 0 2)
  (
    (3 -10 0 2) ; <- duplicate
    (0 -10 0 2)
    (-3 -10 0 2)
  |
    (3 -10 0 2) ; <- duplicate
    (6 -10 0 2)
    (9 -10 0 2)
  )
)

Unit test, Unit test

Note: As of today, it is OK for a duplicated point to have a different radius than the original point.

When writing the file the duplicate point is not automatically added. However, a warning will be displayed if the first point of a section differs from the last point of the previous section.

Unit test

Single point section

A section made of only one point will be treated differently depending on whether the point is a duplicate of the parent section last point or not.

• If it is a duplicate, the section is discarded. Example:

  ((Dendrite)
    (3 -4 0 2)
    (3 -10 0 2)
    (
      (3 -10 0 2)  ; duplicate point
    )
  )
  

  will become:

  ((Dendrite)
    (3 -4 0 2)
    (3 -10 0 2)
  )
  

  See here and here for a more complex case

• If the point is not a duplicate, then the duplicate point is prepended at the beggining of

  the section and the section is considered perfectly valid. See here

  ((Dendrite)
      (3 -4 0 2)
      (3 -10 0 2)
      (
         (3 -100 100 4)  ; not a duplicate point
      )
  )
  

  will be equivalent to:

  ((Dendrite)
      (3 -4 0 2)
      (3 -10 0 2)
      (
       (3 -10 0 2)    ; added duplicate
       (3 -100 100 4)
      )
  )
  

Single child section

Section with only one child section will have their child merged with.

((Dendrite)
 (3 -4 0 2)
 (3 -6 0 2)
 (3 -8 0 2)
 (3 -10 0 2)
 (
   (3 -10 0 2)  ; merged with parent section
   (0 -10 0 2)  ; merged with parent section
   (-3 -15 0 2) ; merged with parent section
   (
     (-5 -5 5 5)
     |
     (-6 -6 6 6)
   )
 )
)

will be interpreted the same as:

((Dendrite)
 (3 -4 0 2)
 (3 -6 0 2)
 (3 -8 0 2)
 (3 -10 0 2)
 (0 -10 0 2)
 (-3 -15 0 2)
 (
   (-5 -5 5 5)
   |
   (-6 -6 6 6)
 )
)

Unit test

Empty siblings

File with empty siblings are handled correctly:

((Dendrite)
 (3 -4 0 2)
 (3 -6 0 2)
 (3 -8 0 2)
 (3 -10 0 2)
 (
   (3 -10 0 2)
   (0 -10 0 2)
   (-3 -10 0 2)
   |       ; <-- empty sibling but still works
  )
 )

will be interpreted the same as:

((Dendrite)
 (3 -4 0 2)
 (3 -6 0 2)
 (3 -8 0 2)
 (3 -10 0 2)
 (0 -10 0 2)
 )