Tools for plot 3d Quiver Plot Arrows on a 3d + time acquisition

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#1

Dear Forum,
I am dealing with fluid/cell motility in 3D, by now we are not interested in 3d tracking.
I would like to have a good tool to plot quiver 3d arrows (let’s say coming from x,y,z coordinates - much better with a physical unit - and with velocity fields vectors) on 3d (multi-focal) over time acquisitions.
Someone here has some experience with plotting and handling 3d+t visualization and could suggest me some approaches/tools/softwares?
I was playing with Matlab but the quiver was quite good but the 3d rendering of the cells was poor, but it could be also my fault.

I am open to whatever programming languages, even if I would prefer Matlab or Python or Fiji environment.
Thanks,
Emanuele

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#2

Does that mean that you’d like to plot a 3D Quiver plot overlaid onto a volume rendering of your cells? I’d also be interested in a good solution.
Maybe the latest developments in #sciview can help here (but you’d still need to create some 3d mesh model of your quiver plot arrow objects…)

For plotting 3D Quiver plots in a simple coordinate system (without volume data) in Python, did you try matplotlib yet?

https://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html#quiver

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#3

Hi Emanuele,
recent release of Matlab can do volume rendering but sadly it can’t be really combined with other data types, such as quivers. Some other commercial packages can work with those (for example, Amira and may be Imaris).

If I would do that in Matlab or matplotlib I used one of these options:

  1. segment the cells of interest and generate surfaces for each time point. After that visualize those surfaces together with quiver arrows. You probably have to write a small GUI to control the visualization at each time point.
  2. Instead of surfaces/volume rendering use the max intensity projection. You can generate the projection and show it as an orthoslice under the quiver arrows. It may give good idea about your original data and correlate it with the arrows.

Ilya

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#4

Hi @emartini,

this actually sounds like a perfect job for #sciview :sunglasses: We do not actually have quiver plots yet, but @ulman recently integrated arrows, so that would probably be a relatively easy task. You can actually overlay any geometry with your volumetric data.
Would you be able to share some data so we can play around?

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#5

Dear all,
thank you for all the suggestions!
this month I am out of the office, at the end of the month I will be back to my desk and elaborate more on this topic.
Thanks a lot,
Emanuele

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