Changes between Version 21 and Version 22 of u/erica/Amira

Timestamp:

11/11/15 21:15:17 (10 years ago)

Author:

Erica Kaminski

Comment:

—

u/erica/Amira

@@ -1 +1 @@
 = 11/7/15 - Disperse algorithm =
 
-After reading through the Disperse documentation, it is clear that Disperse is better than Amira for identifying filaments. This is because way Disperse considers each cell in the grid in relation to others, whereas Amira applies a black/white mask to the data.
+After reading through the Disperse documentation, it is clear that Disperse is better than Amira for identifying filaments. This is because Disperse considers each cell in the grid in relation to others, whereas Amira applies a black/white mask to the data.
 
 Here is a brief outline of the Disperse algorithm:
@@ -18 +18 @@
 The idea is that pairs with lower 'persistence' (i.e. below the persistence threshold) are topologically weak structures -- meaning that they would not persist above some noise added to the data set. Even weak noise would disrupt the extrema in the pair such that they may no longer be extrema and thus the pair would be destroyed. Filtering the data using persistence is a way of keeping topologically relevant structures in the data set. Now, using the 'mean density' as a persistence threshold essentially gets rid of all data point pairs that are below the mean density (density is strictly positive).
 
-Now between all persistence pairs that survive, arcs are drawn that connect saddle points to the 2 extrema which connect to them (each saddle point is connected to exactly 2 extrema). Arcs are tangent lines to the gradient field in the data set. ''Filaments are, by default, arcs that connect a saddle point with 2 maximum''. 
+Now between all persistence pairs that survive, arcs are drawn that connect saddle points to the 2 extrema which connect to them (each saddle point is connected to exactly 2 extrema). Arcs are tangent lines to the gradient field in the data set. '' Filaments (in Disperse) are, by default, arcs that connect a saddle point with 2 maximum''. 
 
 = 11/6/15 - Using Amira with the mean density to create filaments =