Hi all!
I have been using the 3D Image Suite's Spot Segmentation tool to count
punctate ROIs in a z-stack. In trying to write a macro that allows the user
to optimize parameters, I discovered that changing the macro recorded value
for the field labelled "Seeds radius (automatic)" did not seem to affect
the segmentation result. I then tried to input different values directly
into the dialog box and found that this did not affect the result either.
Perhaps there is an issue with the variable meant to hold the input? I
would like to be able to use "Seeds radius (automatic)" to exclude seeds
smaller than 1 pixel, thus getting rid of the local maxima created in the
seeds stack, from the background in the original image. Included in the
dropbox links is the 3D Local Maxima seeds stack created using 3D Fast
Filters --> Local Maxima with a kernal size of 3 pixels in x, y and z. Also
included is a composite stack with the segmented 3D ROIs in red and the
original image in green. There is a clear overcount of ROIs that might be
remedied by size excluding the seeds.
Any ideas or suggestions on how to get the values recognized when the
plugin is called from the macro, would be greatly appreciated!
Best,
Feriel Presswalla
Kellogg Eye Center
University of Michigan
---
*Links to files* -
https://www.dropbox.com/s/vdpdndu9tx22jbm/3D_MaximumLocal1.ome.tif?dl=0-
https://www.dropbox.com/s/xuyy39qktbuoebh/Composite1.ome.tif?dl=0*ImageJ version 1.5e and Java version 1.6.0_24*
*Parameters used in the 3D spot segmentation plugin:*
run("3D Spot Segmentation", "seeds_threshold=8000 local_background=0
radius_0=2 radius_1=4 radius_2=6 weigth=0.50 radius_max=3 sd_value=1
local_threshold=[Gaussian fit] seg_spot=Maximum watershed volume_min=1
volume_max=1000000 seeds=3D_MaximumLocal spots=raw radius_for_seeds=2
output=Both 32-bits");
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html
Locked
