[Murg] Connectionists: NEURON Summer Course registration deadline approaching (fwd from ted.carnevale@yale.edu)

[Eugen Leitl]

On Thu, Apr 07, 2005 at 01:39:08PM -0500, Randal A. Koene wrote:
> Hi Eugene and Jesse,
> 
> I was quite happy to see the clarity and precision of the hippocampal 
> images produced. It is great to be able to zoom into the individual 
> synapses so well. For myself the problem is currently simply one of 

There's certainly an embarrassment of riches in regards to structural data.
Also, we see that the ultrastructure level looks very good, and we have every
reason to infer smaller structures (transmembrane receptor distribution and
individual channel modifications) remain in pristine shape. So that's the
good news.

The bad news is that assembling TEM slices alone and segmenting out shapes
does not result into something we can plug into a simulation. We're lacking
parameters for those shapes. That's okay, though, it's something we've been
expecting.

> expertise. Mine is at the level of dendritic/axonal structure (see
> http://rak.minduploading.org:8080/caspan) and neuronal systems (see 

By observing the system in action before scanning it you can extract these
parameters. You can even build rules, given from empiric data how these
parameters cluster, and how subtle morphological differences which can still
be resolved in TEM can be used for labels for parameters. 

I don't understand the problem set at all, but I think assuming above will be
enough to salt your TEM slice stacks is way too optimistic.

> http://askja.bu.edu:8080/catacomb/). I have yet to reach the level where I 
> can recreate something using this amazing morphological detail about the 
> individual cells. So, I tend to observe until I can make more useful 
> comments.

What do your peers say to the idea of building 3d morphology models from
vitrified neurotissue TEM stacks?
 
> Cheers,
>        Randal
> 
> On Thu, 7 Apr 2005 cat13 at illrepute.org wrote:
> 
> >On Thu, 7 Apr 2005, Eugen Leitl wrote:
> >
> >>On Thu, Apr 07, 2005 at 11:35:04AM -0400, cat13 at illrepute.org wrote:
> >>>
> >>>I did not reply because I wasn't sure what to say.  I don't know what I'm
> >>>looking at in the images - for example, I don't know how to identify the
> >>>boundaries of the cells here:
> >>>http://www.alcor.org/Library/images/embrain03.jpg
> >>
> >>It's not just the segmentation issue, we don't know the properties of
> >>whatever pieces of neuroanatomy we can segment. This isn't a worm, where
> >>everything is known and doesn't need labels, since in standard
> >>locations/connectivity.
> >
> >What information IS available for turning these images into a working
> >model of anything?
> >
> >And what missing information would be most useful to have?
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Eugen* Leitl <a href="http://leitl.org">leitl</a>
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