http://imagej.273.s1.nabble.com/areatree-results-LB-cable-length-tp5006194p5006219.html
> Thanks. I don't know whether I should use the LB measurement though: on one hand it removes the "artificial" jitters but on the other hand does not ignore the natural winding of dendrites that can slightly bend and turn in the tissue? In some of my dendrites, the cable length and the LB cable length are very different (LB half the cable length)... do you think it is always better to choose the LB measurement? I need to know the length of the dendritic shaft in order to calculate spine density.
The LB measurement can be too low if you neurons don't branch a lot. It is there to provide a reference. A proper measurement would be the cable length of a tree smoothed by convolving with a gaussian, or as a reasonable approximation, a running three-point average that would remove most jitter. The latter, if not available in TrakEM2 (I thought it was, as a "smooth" measurement?), would be quite trivial to compute with a script.
>
>
>> On Mon, Jan 20, 2014 at 6:35 PM, Albert Cardona <
[hidden email]> wrote:
>> The Lower Bound (LB) cable length is a way to approximate the minimal possible cable length that the tree could have. Consists of measuring as straight lines the distance between end node and branch node, branch node to branch node, and branch node to root, and adding them all up.
>>
>> The main effect of the LB measurement is that the jitter from the human's innaccuracy and the jitter from the image registration errors are almost completely removed. This is particularly important for EM reconstructions from serial sections; if you use light-microscopy image stacks the jitter cannot be much and is likely not significant.
>>
>> There is an example of this measurement in supplemental figure 15, and an a schematic of its measurement in suppl. figure 16 of this paper:
>>
>>
http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2072.html>>
>> "Elastic volume reconstruction from series of ultra-thin microscopy sections"
>> Stephan Saalfeld, Richard Fetter, Albert Cardona & Pavel Tomancak
>> Nature Methods 9, 717–720 (2012) doi:10.1038/nmeth.2072
>>
>> In there, we demonstrate how better image registration brings the cable length of a hand-reconstructed neuronal arbor closer to the lower bound measurement. The latter stays nearly constant for all image registration techniques used, which endorses its robustness.
>>
>> Albert
>>
>>
>>
>> 2014/1/20 Luisa de Vivo <
[hidden email]>
>>> Hi,
>>>
>>> does anybody know the difference between Cable length and LB Cable length
>>> in the Areatree results window of TrakEM2?
>>> Thank you very much,
>>>
>>> Luisa
>>>
>>>
>>> --
>>> Luisa de Vivo, PhD
>>> Department of Psychiatry
>>> University of Wisconsin
>>> 6001 Research Park Boulevard
>>> Madison WI 53719
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>>
>>
>> --
>>
http://albert.rierol.net>>
http://www.ini.uzh.ch/~acardona/>
>
>
> --
> Luisa de Vivo, PhD
> Department of Psychiatry
> University of Wisconsin
> 6001 Research Park Boulevard
> Madison WI 53719
>