Mercurial > repos > imgteam > imagej2_watershed_binary
comparison imagej2_watershed_binary.xml @ 0:b143159845b4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
| author | imgteam |
|---|---|
| date | Tue, 17 Sep 2019 17:02:55 -0400 |
| parents | |
| children | 5b154339fd90 |
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| -1:000000000000 | 0:b143159845b4 |
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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__/imagej2_watershed_binary_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> |