

Are There Cell-Scale Anatomical Coordinate Systems? - JabavuAdams

For to accurately and repeatably describe positions, you need to agree on some kind of coordinate system.<p>Anatomical coordinate systems are tricky, because you&#x27;re people are deformable and different.<p>If I wanted to be able to say &quot;drive down this artery 1000 cells, and then go to this cell in the wall.&quot; Is there an existing coordinate system that  could do this? Are there software libraries?
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schrodingersCat
Yes and no. Yes, there are general tissue-level anatomical structures that
have consistent, predictable topologies. No, there's not a standard way to map
these onto a cell scale coordinate system easily. When you are talking about
cell-level anatomy, you can almost think of things as being slightly
disordered, with the disorder increasing the smaller in scale you go. Most
tissues have constant turnover of cells, further complicating the concept of a
coordinate system. Some examples where there is a consistent (almost)
unchanging anatomy would be in neurons and stem cell germ layers.For germ
layers, simple 3D coordinates would work. If you could figure out a coordinate
system that works for neurons, you would get a Nobel prize. Sorry I couldn't
help you more. What exactly are you hoping to do with said library?

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JabavuAdams
I'm trying to imagine how you'd tell a cell-scale machine "go to that cell ...
that one there", rather than "drive along this chemical gradient", or "bounce
around until you match this receptor."

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schrodingersCat
Well that's an even more complicated problem. That would depend on what type
of cell you wanted to target and in what tissue. Most tissues are quite
heterogeneous and constantly remodeling. Even if you could get the coordinates
of a particular cell before it moved, targeting the specific cell (and not the
others that are likely to be present in the vicinity)is a problem unto itself.
Don't diss diffusion and biorecognition, they're quite effective. In my mind,
any robot designed on the scale to target individual cells would have to
mostly rely on circulation, diffusion, and chemistry to target a particular
cell type. The mechanics are far from deterministic on the nano scale. I
highly recommend this book if you're considering a project like this:
[http://www.garlandscience.com/product/isbn/0815341636](http://www.garlandscience.com/product/isbn/0815341636).
If this is for a visualization or a game, I would just fake the coordinate
system.

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JabavuAdams
Thanks!

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abhikshah
> For to accurately and repeatably describe positions

IMO, for most use cases, you don't need to describe positions; you provide
something analogous to a SQL where clause.

Most querying in cell biology appears to content-based rather than coordinate-
based. "drive down this artery 1000 cells" is not useful because your target
might be 1010 cells down next week. Instead, you might say "drive down this
artery until you find a cell with this particular receptor on the cell wall."
Rather than keeping track of how many cells you've passed, you randomly bounce
around the artery until you bind to a compatible receptor.

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JabavuAdams
Good points. I'm coming from a pretty speculative direction where I'd want to
enforce invariants, like: repair this tissue in-situ so that its thickness is
always between x and y. Or make sure the density of this kind of cell in this
region is at least A, and no more than B.

Basically, 3d modelling for tissue. How do you specify the reference model?

