Hello everyone,
I have cryo tomograms which shows actin bundles as features of interest. I need to segment them and create a 3D representation. I used some software (IMOD, EMAN) and got some preliminary segmentation but i still have trouble in getting a 3D representation. Need some advice and input on this - what other free or a user friendly software i can use or how can i perfect the segmentation in IMOD/EMAN or is there any other option at all.
Any help would be great.
Thanks in advance.
Check out the new release of 3D Slicer. There are some new features for automatic segmentation of 3D representations.
Lambert Zijp - Here you go - Hope you can see something in that resolution.
Are there two filaments vertically oriented?
Is this the best resolution and the color depth is only 8 bits?
If so, segmenting them is difficult. Standard software, like 3D slicer, will not be able to. You could try a Frangi filter in Matlab/Octave, but I'm afraid some processing needs to be done before... Not easy!
Lambert Zijp - Parallel actin filaments occur in bundles throughout the tomogram in different angles.This is the resolution, the more I zoom in,the more I lose the resolution. And that's an issue i'm facing. Do you suggest something else?
Before suggesting anything, I need to know what I'm looking at. Can you draw the filaments in the picture? Or describe what they look like?
So the picture you posted is original data, i.e. no downsizing or brightness/contrast adjustments?
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