Surface reconstruction with subdivision of IMM compartments

[Kathir-66]

Hi, Thanks again for making the pipeline

I want to make surface reconstructions with subdivision of IMM like you make in the figures in your paper. Particularly like the figure 4A.

I went through the morphometrics_Stats.py and mitochondria_statistics.py, I could only find the code to separate the IMM into its sub compartment and perform statistical analysis. Since being beginner in python maybe I missed something.. so your clarity here would be helpful

If it is not already included in the pipeline. I would like to know how to proceed once I divide the IMM into its subcomponents how to feed them into the VTK files to visualize them !

Thanks again for your help!

[bbarad]

Hi Kathir,

The statistical analysis and the visual analysis are almost entirely separated in the workflow, so you are correct that the statistics scripts don't do anything for sub-compartmentalizing for visualization (only for stats). For the visualization in a step-wise function, I load the vtp meshes into paraview and adjust the coloring to display step functions at the cutoffs I am choosing for quantification. You can also change it so that only those triangles are visible by adjusting opacity instead of color. I am far from the biggest expert in the world on doing this kind of paraview image generation so there may be a better way, but this worked for me!

Thanks, Ben

[bbarad]

@mmedina300 do we have a written protocol for this? I am thinking of expanding my tutorial on the lab website to include more edge case stuff like this.