Changes between Version 16 and Version 17 of u/erica/Amira


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Timestamp:
11/11/15 15:25:13 (9 years ago)
Author:
Erica Kaminski
Comment:

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  • u/erica/Amira

    v16 v17  
    55Here are some results testing different thresholds in auto skeletonization mode, and comparing them to Federrath's figure (the paper that contains this figure is attached to this page).
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    7 [[Image(compare5.png, 95%)]]
     7[[Image(compare5.png, 50%)]]
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    9 [[Image(compare2.png, 95%)]]
     9[[Image(compare2.png, 50%)]]
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    11 [[Image(compare1.png, 95%)]]
     11[[Image(compare1.png, 50%)]]
    1212
    13 [[Image(comparept01.png, 95%)]]
     13[[Image(comparept01.png, 50%)]]
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    2121Amira segments the data to do skeletonization. This means it throws out pixels below a certain user defined threshold. Of the remaining pixels it 1) finds a centerline through the data that, 2) is through the middle, and then 3) thins this line to be 1 pixel across. This is all to retain "homotopy" of the filamentary network. This is not ideal for column density data: as the threshold is lowered to account for lower density pixels, the structures get blown out and the skeletonization algorithm breaks down. Here are some images that gradually increase the threshold to illustrate this (smaller to larger thresholds):
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    23 [[Image(2757full.png)]][[Image(2757thresh.png)]]
     23[[Image(2757full.png, 50%)]][[Image(2757thresh.png, 50%)]]
    2424
    25 [[Image(6330image.png)]][[Image(6330thresh.png)]]
     25[[Image(6330image.png, 50%)]][[Image(6330thresh.png, 50%)]]
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    27 [[Image(10228full.png)]][[Image(10228thresh.png)]][[br]]
     27[[Image(10228full.png, 50%)]][[Image(10228thresh.png, 50%)]][[br]]
    2828 
    29 [[Image(29360full.png)]][[Image(29363thresh.png)]]
     29[[Image(29360full.png, 50%)]][[Image(29363thresh.png, 50%)]]
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    3131From this, one can interactively click on the filament that is of interest, and get the resultant statistics for it. However, to sample a wide range of densities, this requires multiple thresholding steps, and probably performs worse than disperse.
     
    3333As a different project, one might want to track filaments in a 3d data cube and compare to the number of filaments found in projection. Here the projections might be evaluated using disperse. Take a look at this image of a neuron:
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    35 [[Image(amira.png, 68%)]]
     35[[Image(amira.png, 50%)]]
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    3737If the hypothesis that all filaments are r=0.1 pc across is true, then maybe one gets cleaner segments; that is, filamentary structure that is more amenable to this segmentation approach. Also, one could use a physically meaningful density threshold to segment the data (i.e. the density at which molecular hydrogen can form efficiently). However, for now this project is going to be put on hold.