[3dem] Workflow for TEM volumes containing noise in Amira?

[Charlotte Hamngren]

Dear 3DEM community,

I hope you are well!

I am using Inspect3D together with Amira for the 3D visualisation of
membrane structures inside the a cell: ER and Golgi, etc. My raw data is a
TEM tilt series (room temperature) acquired with the FEI Tomography
software. The membranes in the reconstructed volume (SIRT 20 iterations)
are clearly visible by eye, but the reconstructed volume is quite noisy
since the sample cannot be heavily contrasted. I would like to automate the
visualisation process as much as possible before turning to manual
segmentation as a last resort. The Volume rendering process in Amira
suffers a lot from the noise, so I am looking for advice. Is it a waste of
time to try to de-noise the volume?

Is anyone else doing something similar? Can you suggest a usable workflow
for working with TEM volumes containing noise in Amira (a publication or
your own experience perhaps)?

Stay safe,
Charlotte
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