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kephale / napari-tyssue

This is a napari plugin that supports the 3D tissue simulator, tyssue
BSD 3-Clause "New" or "Revised" License
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Use case: simulate tissues undergoing topological changes #4

Open haesleinhuepf opened 1 year ago

haesleinhuepf commented 1 year ago

Hey @kephale ,

you asked for use-cases, so here you go. I'd like to simulate tissues undergoing topological changes (e.g. a T1-transition or a cell-extrusion). My ideal format would be a 3D+t label image where some cells change their neighborhood-relationship. It's kind-of-important that the data is true 3D; not just a single-layer of cells (boring ;-) ).

It'd like to characterize such changes over time quantitatively using pyclesperanto in napari and need a well simulated dataset to see if it's doing the right thing.

Do you think this could be done using tyssue?

Thanks!

Best, Robert

kephale commented 1 year ago

I'll bring in @glyg and @sophietheis for this question.

The existing demos allow you to have 2D sheets in 3D space, but I have not seen any examples with 3D cells.

If your use cases is about generating synthetic data, then you might not really care about the UI/graphics since you can always rerender the outputs. PhysiCell or CompuCell3D might be worth considering as alternatives (but those have C++ engines). That said, I am definitely interested in a Python-centric approach.

haesleinhuepf commented 1 year ago

If your use cases is about generating synthetic data, then you might not really care about the UI/graphics

I tend to make user-friendly GUIs for everything I use because most of my collaborators can't code 😉 Thanks for the hints! I'll check those out.

glyg commented 1 year ago

Hi @haesleinhuepf tyssue can do "true 3D" and topological changes therein (like creating a "skutoid") You can look into this notebook for 3D https://github.com/DamCB/tyssue-demo/blob/master/06-Cell_Division.ipynb

We can have monolayer and multilayer

Simulating extrusion is super hard though, because the topology changes are complicated! In general, for robust 3D modeling, we would need to add some kind of remeshing tool included in tyssue. I'd love to have that but it is not here yet.