These are chat archives for fiji/fiji

12th
Apr 2017
Jan Eglinger
@imagejan
Apr 12 2017 06:55
@GregT102 Fast Neurite Tracer looks to me like a standalone program, not a plugin for Fiji/ImageJ. Unfortunately, there seems to be no source code on the linked project page, just the binary distribution. I second the advice to have a look at Simple Neurite Tracer, though.
Curtis Rueden
@ctrueden
Apr 12 2017 15:54
Does anyone know: is there a such thing as "fill small holes"? I.e.: fill holes, with a maximum bound? It seems like it would be useful for situations like the following:
Robert Haase
@haesleinhuepf
Apr 12 2017 15:55
Something like binary closing?
Curtis Rueden
@ctrueden
Apr 12 2017 15:56
mask.png
There, finally got a good version of the image posted.
@haesleinhuepf I guess? With Ops the radius is configurable eh?
It's surprising to me that close does not mangle the edges of large structures.
Jan Eglinger
@imagejan
Apr 12 2017 15:58
The problem: the holes between the objects are sometimes smaller than the "internal" holes that you like to fill.
Robert Haase
@haesleinhuepf
Apr 12 2017 15:58
You know, I'm not an Ops-expert, but: all you need is erosion and dilation with configurable radii or run in a loop...
Jan Eglinger
@imagejan
Apr 12 2017 16:00
yes, close (or even dilation/erosion with different radii) can be helpful, but often some smoothing/convolution, followed by maxima detection performs better IMHO
Robert Haase
@haesleinhuepf
Apr 12 2017 16:02
Huh, I'd like to see that in action 🙃
Curtis Rueden
@ctrueden
Apr 12 2017 16:02
@imagejan I agree that filling holes up to some constant global size does not fully solve the image above. But it is still better than an unbounded fill holes.