thorstenwagner / ij-shape-filter Goto Github PK

Hello, thanks for this useful plugin.

I have some 32-bit TIFFs (produced by Ilastik's pixel classification) that I want to convert to binary images in order to perform a segmentation. I use the Shape Filter plugin to exclude some objects (e.g. those touching the borders). I have observed that the plugin only works correctly if the "Black Background" option is checked in the dialog box, independently from the value of the "Black Background" global option of ImageJ. For example, the following macro produces an empty white image, while I would expect it to retain all objects except the one touching the borders. It works as expected only if I add black_baground to the last command.

setOption("BlackBackground", false);
open("/home/gabriele/tmp/example.tif");
setThreshold(0.50, 1.00);
run("Convert to Mask");
run("Shape Filter",
"area=0-Infinity " +
"area_convex_hull=0-Infinity " +
"perimeter=0-Infinity " +
"perimeter_convex_hull=0-Infinity " +
"feret_diameter=0-Infinity " +
"min._feret_diameter=0-Infinity " +
"max._inscr._circle_diameter=0-Infinity " +
"area_eq._circle_diameter=0-Infinity " +
"long_side_min._bounding_rect.=0-Infinity " +
"short_side_min._bounding_rect.=0-Infinity " +
"aspect_ratio=1-Infinity " +
"area_to_perimeter_ratio=0-Infinity " +
"circularity=0-Infinity " +
"elongation=0-1 " +
"convexity=0-1 " +
"solidity=0-1 " +
"num._of_holes=0-Infinity " +
"thinnes_ratio=0-1 " +
"contour_temperatur=0-1 " +
"orientation=0-180 " +
"fractal_box_dimension=0-2 " +
"option->box-sizes=2,3,4,6,8,12,16,32,64 " +
"exclude_on_edges");

Thanks in advance.

Add checkbox "Scaled Units" for filtering in scaled units.