Microscopy Optics and Image Analysis Seminar

* * *

vedo

A python module for scientific analysis and visualization of 3D data


Marco Musy, Sharpe Lab - 9th November 2021

Why slide2
Where slide3
What slide4
How slide6
CLI - Meshes slide8
CLI - Meshes slide9
CLI - Volumes slide10
slide_ex_warp
clone viewer slide14
clone viewer bare bones slide14
clonal analysis1 slide16
clonal analysis2 slide17

Resulting force field

[drag & pan with left button, zoom with right button, press r to reset camera]

Resulting displacement field

[drag & pan with left button, zoom with right button, press r to reset camera]

ex. lego
ex. vol probing
heart analysis slide16

Interactivity and Animations

Renderings can include buttons, sliders etc. and react via callback functions

Limb Fitter


Fitting mouse limb outlines to create a continuous timecourse

 libfitter
vedo2d
gene mapper slide16

Integration

vedo supports FEniCS (FEM package) and is compatible - or has examples - with many other libraries:
Qt, pymeshlab, SHtools, nevergrad, iminuit, meshio, trimesh, pyvista, fury etc...

fenics1 pymeshlab1 vpolyscope

web_jupyter

Conclusion


The package is by now in a reasonable good state for general use

 ● Proved useful in our lab

 ● Would love to advertise it within EMBL

 ● Find if there’s any point of contact with ongoing EMBL research

 ● Happy to offer support!

rotating_embryo

Thanks!


embl_logo    sharpe_logo