[ImageJ-devel] Labeling / segmentation proposal for imglib

[Lee Kamentsky]

Hi Albert,

I could see how using ShapeLists could work well for us for most cases 
seeing that we mostly use 2-d. It looks to me like you need one shape 
per z-plane in 3-d? I am thinking that there is still some utility in 
having something that represents the segmentation or labeling as a 
whole. In that scheme, the shapes would be views into the underlying 
representation of the labeling. Finally, I think there is some utility 
to a localizable cursor that doesn't use shapes as an intermediate 
because that sort of cursor would only visit labeled pixels whereas the 
shape cursor, at best, visits all pixels in the shape's bounding box 
(and for naive uses, might visit all pixels in the image). Some 
labelings, such as those on neurons, are sparse within their bounding 
boxes and, it seems to me, would require many calls to 
java.awt.Shape.contains(x,y).

--Lee

On 11/16/2010 5:02 PM, Albert Cardona wrote:
> 2010/11/16 Lee Kamentsky<leek at broadinstitute.org>:
>> Now I do ;-)
>>
>> I think the ShapeImage container is not appropriate since it's based on
>> java.awt.Shape - I think that segmentation results are too general to be
>> represented by shapes, the ShapeListCache doesn't scale to hundreds of
>> labels per image,
>
> The cache is per cursor, and simply stores the last N desired visited locations.
>
>
>> and the typical algorithms used on these sorts of results
>> might not be efficient.
>
> Have you tried it? I have. Currently, giant (>5000) areas are rendered
> in 3D using marching cubes and it works great.
>
>
>> Also, using java.awt on the Mac will cause
>> difficulties for CellProfiler and others because of some unfortunate
>> implementation decisions in awt and Mac OS beyond our control.
>
> java.awt.Shape is an interface. That shouldn't cause any problems.
> java.awt.geom.Area, java.awt.Rectangle, and others, are in the
> java.awt package but have nothing to do with the GUI awt classes. They
> can be used cleanly.
>
>
> You may want to give it a second look and run some tests.
>
> Albert
>