Turner Ca1 readme file.
Duncan Donohue
5-29-01
This file documents the changes made to Ca1 in vivo cells from the Turner archive. Upon close inspection some of these files were found to have errors or irregularities giving them biologically impossible or implausible morphologies. Most of these errors have to do with segment types. They can be categorized as follows.
1. Incorrect sub tree type: Terminal branch of tree of a different type than preceding segments. Type changed to that of parent.
2. Incorrect intermittent type: Internal section of a tree has different type than both preceding and following segments. Type changed to that of rest of tree.
3. Transition type error: Compartment or small group of compartments have different type than both preceding and following segments which also differ from each other. Usually found at soma. Differentiated from type 1 error by relative sizes of segments and cell morphology (apical, basal, ect.). Changed to type of preceding or following segment with closest diameter.
4. Random link: Single compartment (usually long) connecting two branches of different types in a biologically implausible way. Link is removed. Branch that is not otherwise connected to the soma is attached to a branch of its own type at or near its maximum diameter with the shortest segment possible (determined by visual inspection only).
5. Random segment: Single segment (usually small) of different type attached to branch or soma. Segment removed, all lines following removed point renumbered and re-linked as necessary.
6. Incorrect starting type: Line one in SWC file is not of type 1. If soma exists file is reorganized so that it starts in the soma and morphology is retained. If no soma exists one is created.
7. Other: Error particular to individual cell, error corrected and explained.
The following is a detailed account of changes made to the files by cell number then error type. The segment number followed by it's type in ( ) is given for the segments changed. * designates errors that have not yet been fixed. Other irregularities which may or may not be errors are listed on an additional indent.
n400 5 2788(-1) out of (1)
3 2795(4) to (1)
7 129(4) removed (random and odd dia)
n401 1 4451-4486(4) to (3)
Possible type 3 error (4448-4450), but tree heads in basal direction??
2 951, 952(1) to (4)
3 950(4) to (1)
951 and 952 changed otherwise there is odd apical branching
950 changed otherwise there is a basal tree off of an apical one
2 3989(1) to (4)
Possible type 4? (long single segment at odd angles)
n402 3 2, 1884(-1) to (1)
3 3, 4, 430, 431(-1) to (3)
n403 2 3084-3086(-1) to (3)
Odd connection, long straight, ziz-zag at end.
3 4055(-1) to (3)
n404 2 2(-1) to (1)
3 4946(-1) to (3)
n405 3 2730, 3223, 3777, 4312(-1) to (3)
n406 2 17, 110(1) to (4)
3 2071, 2272, 2607(-1) to (3)
n407 3 2, 349, 1448, 5226(-1) to (3)
3 4549(4) to (3)
5 353, 354(1)
354 was at same location as 352 and was also removed
n408 good
odd segment at 1380. It is preceded and followed by segments at the same location which morphologically is a trifurcation.
n409 good odd type ones at 1322-1330, 1435-1458? Dia.=.1 Has several type 3 stems off of it.
n410 2 3142(4) to (1)
n411 6 1-16, 1617-1624(4) to (1)
cell had no type 1 segments. 1624 chosen as soma cut off arbitrarily at diameter drop of 2.35 to 1.65.
1 4614(-1) to (4)
n412 good
n413 3 2778, 3178, 3374(-1) to (3)
n414 3 1115(-1) to (3)
n415 3 2870(-1) to (3)
1 3485, 3486(1) to (3)
3 3487(-1) to (3)
n416 3 4(-1) to (3)
n417 good
line 3 to 4 connection odd, long, big diameter jump, makes soma odd shape.
n418 3 3, 4, 1334-1336, 2153(-1) to (3)
5 2155(1) off of (3)
n419 good
n420 good
n421 good
n422 3 3, 4, 5(-1) to (3)
n423 7 2195(4) connected to 2194(4)