[Chimera-users] Watershed segmentation of volumes

[Thomas Goddard]

Hi Jeff,

There is no watershed or flood-fill type of method in Chimera for 
segmenting volume data.  This is on our (very long) list of features to 
develop though.

    Tom

Jeff wrote:
> tom,
>
> i hate to keep piling on questions, but how hard would it be to have a 
> feature where one places a chimera marker, and then has some sort of 
> algorithm expand to 'fill' the space, kind of an isosurface problem 
> (or does this already exist)
>
> i have 'voids' in some of my maps (stained sections) which i think 
> correspond to protein, like one sees in negative stain (the positive 
> values/density in the map correspond to stain; an enclosed void 
> (density more or less = 0 or close to it) is thought to represent the 
> actual protein, which was covered in stain, kind of like 'magic shell' 
> on ice cream - or think of dairy queen cone, dipped in chocolate that 
> then solidifies), and would like some way to 'grow' a blob in the void 
> (or at least try)
>
> does this already exist? i have a buddy who does level set methods who 
> is often looking for ways to use his library, but i thought i should 
> ask you first if there is some functionality like this
>
> -jeff