Are There Cell-Scale Anatomical Coordinate Systems?

https://news.ycombinator.com/item?id=6021607

by JabavuAdams • 13 years ago

8 6 13 years ago

news.ycombinator.com

For to accurately and repeatably describe positions, you need to agree on some kind of coordinate system.

Anatomical coordinate systems are tricky, because you're people are deformable and different.

If I wanted to be able to say "drive down this artery 1000 cells, and then go to this cell in the wall." Is there an existing coordinate system that could do this? Are there software libraries?

schrodingersCat2• 13 years ago

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?

JabavuAdams3• 13 years ago

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."

schrodingersCat2• 13 years ago

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. If this is for a visualization or a game, I would just fake the coordinate system.

abhikshah• 13 years ago

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.

JabavuAdams3• 13 years ago

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?

Are There Cell-Scale Anatomical Coordinate Systems?

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