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planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
author iuc
date Sun, 11 Oct 2015 14:06:05 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_watershed_binary" name="Watershed segmentation" version="@WRAPPER_VERSION@.0">
3 <description>of binary image</description>
4 <macros>
5 <import>imagej2_macros.xml</import>
6 </macros>
7 <expand macro="fiji_requirements" />
8 <command>
9 <![CDATA[
10 python $__tool_directory__/imagej2_watershed_binary.py
11 --input "$input"
12 --input_datatype $input.ext
13 --black_background $black_background
14 --jython_script $__tool_directory__/jython_script.py
15 --output_datatype $output.ext
16 --output "$output"
17 ]]>
18 </command>
19 <inputs>
20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
21 <expand macro="black_background_param" />
22 </inputs>
23 <outputs>
24 <data name="output" format_source="input" label="${tool.name} on ${on_string}" />
25 </outputs>
26 <tests>
27 <test>
28 <param name="input" value="blobs.gif" />
29 <output name="output" file="blobs_watershed_binary.gif" compare="sim_size" />
30 </test>
31 </tests>
32 <help>
33 .. class:: warningmark
34
35 @requires_binary_input@
36
37 **What it does**
38
39 <![CDATA[
40 Watershed segmentation is a way of automatically separating or cutting apart particles that touch.
41 It first calculates the Euclidian distance map (EDM) and finds the ultimate eroded points (UEPs).
42 It then dilates each of the UEPs (the peaks or local maxima of the EDM) as far as possible — either
43 until the edge of the particle is reached, or the edge touches a region of another (growing) UEP.
44 Watershed segmentation works best for smooth convex objects that don’t overlap too much.
45 ]]>
46
47 </help>
48 <expand macro="fiji_headless_citations" />
49 </tool>