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.

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?

[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?

[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."

[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.

[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?