Changes between Version 14 and Version 15 of u/erica/Amira


Ignore:
Timestamp:
10/11/15 15:12:28 (9 years ago)
Author:
Erica Kaminski
Comment:

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  • u/erica/Amira

    v14 v15  
     1=== October 5, 2015 ===
     2
     3The "auto" skeletonization method appears to take a threshold as an input. This threshold seems to 'mask' (or 'segment') the data so  to only look at voxels with values above this threshold. It then does a 'centerline' analysis, a 'distance map' analysis, and finally a 'thinning' of the skeleton so  that it is only 1 voxel across. To see the paper on this algorithm, it is attached to this page. It is also possible to do these 3 steps on your own in Amira, and thus gain more control over the skeletonization process.
     4
     5Here 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).
     6
     7[[Image(compare5.png, 95%)]]
     8
     9[[Image(compare2.png, 95%)]]
     10
     11[[Image(compare1.png, 95%)]]
     12
     13[[Image(comparept01.png, 95%)]]
     14
     15
     16There are a lot of clear filamentary structure that Amira is missing.
     17
     18
    119=== October 6, 2015 ===
    220
    … …  
    2038
    2139
    22 === October 5, 2015 ===
    23 
    24 The "auto" skeletonization method appears to take a threshold as an input. This threshold seems to 'mask' (or 'segment') the data so  to only look at voxels with values above this threshold. It then does a 'centerline' analysis, a 'distance map' analysis, and finally a 'thinning' of the skeleton so  that it is only 1 voxel across. To see the paper on this algorithm, it is attached to this page. It is also possible to do these 3 steps on your own in Amira, and thus gain more control over the skeletonization process.
    25 
    26 Here 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).
    27 
    28 [[Image(compare5.png, 95%)]]
    29 
    30 [[Image(compare2.png, 95%)]]
    31 
    32 [[Image(compare1.png, 95%)]]
    33 
    34 [[Image(comparept01.png, 95%)]]
    35 
    36 
    37 There are a lot of clear filamentous structure that Amira is missing.
    38 
    3940
    4041