By by Patrick Parker & Deb Watson (Aug. 2010) (UPDATED Dec. 2016: Word doc, PDF)
Trace name | Purpose | Spread sheet name | Tracing tool | Notes |
d##zlen## | Dendrite length | DenLeng |  | From origin of 1st complete protrusion to 1st incomplete. Trace down center until trace exits membrane, then click back to center. Get average of 3 traces, going up and down. |
1. Z-lengths – Z-lengths measure the “analyzed length” of the dendrite.
...
2. Analyzed length – The analyzed length is the distance from the origin of the first complete protrusion to the origin of the last protrusion (whether it is incomplete or complete). This allows for a uniform distance measurement, without overlapping and overcounting.
3. Tracing Z-lengths – 1
a) Blend the first and last section that you will be tracing and adjust the zoom to ensure that the field of view is large enough to follow the entire length of the dendrite without needing to pan. (You can pan across the screen while making z-traces, but it might be easier not to.) 2Once you have the optimal field of view, unblend and look at your first section.
b) Click in the center of the dendrite and scroll upwards, without moving the trace, until the trace exits the membrane. Then Once the trace exits the membrane, click back in the center of the dendrite and continue again, re-centering each time the trace exits the membrane, until you have reached the last section. Then re-center and right-click to end the trace. 3
c) Repeat this process going “downwards,” then “upwards” again. 4“downwards”.
d) Put the 3 2 or 4 z-lengths in the spreadsheet and get the average of the 3 lengths.
e) Trace an even number of z-lengths. The rationale for this: the “upward” trace and the “downward” trace will be slightly different, so an odd number would favor either the “upward” or “downward”, whichever was done more. (Just two traces is fine if they are not significantly different. If there is a big variation, you might want to do 4 traces.)
4. Determining analyzed length – If the origin of the first complete protrusion is section 20, and the origin of the last protrusion (whether complete or which is incomplete) is section 200, then the analyzed length is from section 20 to section 200. If However, if the last protrusion is complete, then the analyzed length can be taken “backwards” to include the complete protrusion. For example, you have the following protrusions:
The analyzed length going “forwards” (from lower to higher section numbers) would be from 20 to 195 – from Going “backwards,” the analyzed length would be from section 200 down to the origin of the first complete (p02) to the origin of the last (p20). However, that would not include p20, which is a complete protrusion. Going “backwards,” the analyzed length would be from section 200 down to section 10.
incomplete protrusion. (See Case 3 below.)
There are many variations. The common possibilities are outlined in the table below:
...
5. Determining analyzed length of dendrites with multiple incomplete spines – Some dendrites will have incomplete spines in the middle of the dendrite, not just at the beginning or end. (This could be due to a missing section, fold, tear, etc.) Determine the analyzed length as above, from the origin of the first complete to the origin of the first incomplete, then start again from the origin of the next complete to the origin of the next incomplete. Each section should also have 3 an even number of z-lengths.
6. Zlen Guideline – On the first and last section of your analyzed length, draw a brightly-colored stamp named “d##_zlenguideline##”. That will serve as a visual indicator of the boundaries of the analyzed length, and it will help when tracing the z-length. It’s easy to click past the boundary and ruin the entire trace if you don’t have a STOP sign.
******
From the Imaging Lab Hand-out (ca. 2008?):
Determining z-length of your dendrite:
...