Merge segmentation data with original tomogram

[Jaime Llodra]

Dear members of this group,

I would like to know how to merge the segmentation data with the original tomogram. By segmentation data I mean the data from the use of the CNN for object classification.

Wish you a nice weekend,

Jaime Llodrá

[Ludtke, Steven J.]

Merge? Not sure exactly what you mean by merge in this context. The results of the segmentation are something akin to a probability map. You could use this to color an isosurface, or threshold it, then apply it as a mask, or combine it with other segmentation maps to make a multi-level segmentation map and use that as a color map.  So, what are you trying to do with it?

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine

Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 

Deputy Director, Advanced Technical Cores                   and Molecular Biology

Academic Director, CryoEM Core

Co-Director CIBR Center

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[Jaime Llodra]

Dear Steven,

Apologies if I'm not clear.

I want to overlay the result of the segmentation into the original tomogram to see how similar/different they are.

Thanks in advance for your help and support.

Jaime 

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/113D31E5-BB8F-49B7-ABC8-45E3F0FECBBC%40bcm.edu.

[Ludtke, Steven J.]

There are a lot of different ways to do this sort of visualization. Here are 2 ideas:

As I said, you can load the tomogram and the segmentation map together into a package like Chimera/X, then use the segmentation map to color the surface/volume as you like. Chimera/X can directly read EMAN2 HDF files (though there may be differences in threshold values if the files are using the new compression scheme).

An alternative scheme would be to threshold the segmentation map at some value you prefer (threshold.binary processor). Multiply the original map by the thresholded volume (basically using it as a mask). Then you can compare the masked and unmasked volumes however you like...  

--------------------------------------------------------------------------------------

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine

Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 

Deputy Director, Advanced Technical Cores                   and Molecular Biology

Academic Director, CryoEM Core

Co-Director CIBR Center

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAPnh1AdteCE%3D2KKyko%2BcdAxKwnrBi02%2B00UTHLsC79Me1ZH0kQ%40mail.gmail.com.

[Jaime Llodra]

Great!

Thanks a lot, Steve

Jaime Llodrá

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/C7DF947D-AEF1-4149-BAA9-256169909793%40bcm.edu.