what to do if the distance or absolute dot product is outside of the scoremat?

[Jingpeng Wu]

Dear Greg,

I see you have a score matrix, called smat_fcwb, with some range index. And you can pull out the score based on the precomputed matrix directly to avoid redundant computation. I am wandering that what do you do if the distance or absolute dot product value is not within the range of the score matrix?

Best,

Jingpeng

[Gregory Jefferis]

On 30 Oct 2018, at 15:22, Jingpeng Wu <jingp...@gmail.com> wrote:

I see you have a score matrix, called smat_fcwb, with some range index. And you can pull out the score based on the precomputed matrix directly to avoid redundant computation. I

The scoring matrix is like a blast scoring matrix (PAM,BLOSUM etc) – it is something that encapsulates the statistics of matches/nonmatches for particular kinds of neurons – fly neurons and in particular fly olfactory projection neurons for that matrix.

If you are using fish neurons, then you can either recompute the scoring matrix (but this means you need to have lots of pairs of neurons that are know matches or non-matches) OR make sure that the spatial scale of your fish neurons is similar to that of the fly neurons e.g. by ensuring that they have a similar size perhaps  just dividing them by a factor of two. NB this is separate from ensuring they are in the same units (microns). I actually had good success for larval fish brain mitral cells just using the regular scoring matrix unmodified.

 am wandering that what do you do if the distance or absolute dot product value is not within the range of the score matrix?

the last distance column applies to all values greater than 50 µm although it is called (40,500]. This is the effect of that all.inside argument in the code here:

https://github.com/jefferislab/nat.nblast/blob/master/R/neuriteblast.r#L542

This also applies to the absolute dot product values although these should be closes (0,1) – the only time there are not is due to numerical precision issues.

Best,

Greg.

--

Gregory Jefferis, PhD

Division of Neurobiology

MRC Laboratory of Molecular Biology

Francis Crick Avenue

Cambridge Biomedical Campus

Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis

http://jefferislab.org

http://www.zoo.cam.ac.uk/departments/connectomics