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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:14:34 +0000
parents 49b5288dcd8c
children
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5f5b7185bc16 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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1 <tool id="imagej2_skeletonize3d" name="Skeletonize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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49b5288dcd8c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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2 <description>with ImageJ2</description>
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3 <macros>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 <import>imagej2_macros.xml</import>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 </macros>
2
49b5288dcd8c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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6 <edam_operations>
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7 <edam_operation>operation_3443</edam_operation>
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8 </edam_operations>
49b5288dcd8c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
49b5288dcd8c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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10 <xref type="bio.tools">imagej</xref>
49b5288dcd8c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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11 <xref type="biii">imagej2</xref>
49b5288dcd8c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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12 </xrefs>
1
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13 <expand macro="fiji_requirements"/>
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14 <command detect_errors="exit_code"><![CDATA[
768825d9034a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 #import os
768825d9034a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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16 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
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5f5b7185bc16 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
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18 ln -s '$input.file_name' '$input_with_ext' &&
768825d9034a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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19 #set output_filename = '.'.join(['output', $input.ext])
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20 touch '$output_filename' &&
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21 ImageJ --ij2 --headless --debug
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22 --jython '$__tool_directory__/imagej2_skeletonize3d_jython_script.py'
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23 '$input_with_ext'
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24 '$black_background'
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25 '$output_filename'
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26 '$input.ext'
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27 && mv '$output_filename' '$output';
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28 ]]></command>
0
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29 <inputs>
1
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30 <expand macro="param_input"/>
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31 <expand macro="black_background_param"/>
0
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32 </inputs>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 <outputs>
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34 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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35 </outputs>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 <tests>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37 <test>
1
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38 <param name="input" value="blobs.gif"/>
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39 <output name="output" file="skeletonized_blobs.gif" compare="image_diff"/>
0
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40 </test>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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41 <test>
1
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42 <param name="input" value="clown.jpg"/>
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43 <output name="output" file="skeletonized_clown.jpg" compare="image_diff"/>
0
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44 </test>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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45 </tests>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 <help>
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47
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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48 .. class:: warningmark
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49
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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50 @requires_binary_input@
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51
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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52 **What it does**
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53
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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54 <![CDATA[
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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55 Skeletonizes a 2D or 3D binary (8-bit) image. As Hanno Homman explains in his paper, binary thinning is
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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56 used for finding the centerlines (”skeleton”) of objects in the input image. The general idea is to erode
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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57 the object’s surface iteratively until only the skeleton remains. Erosion has to be performed symmetrically
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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58 in order to the guarantee medial position of the skeleton lines and such that the connectedness of the
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59 object is preserved. Care has to be taken in order not to create holes or cavities in the object.
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60
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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61 There are two major approaches to image thinning: a) kernel-based filters and b) decision trees. Kernel-based
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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62 filters apply a structuring element to the image and can generally be extended to dimensions higher than 3D,
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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63 to find computationally efficient solutions for 4D and higher dimensions is subject of ongoing research.
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64 Methods based on decision trees are thus far limited to 2D and 3D, but are potentially faster than morphological
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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65 filters, if they are well designed and can find more deletable points at each iteration.
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66
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67 In 3D there are 67,108,864 possible binary combinations of object and background voxels in a 26-neighborhood,
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68 which cannot be completely captured by kernel-based filters. Lee et al. have demonstrated in their work that
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69 their solution, based on a decision tree, can handle all these cases correctly and find all deletable surface
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70 points at each iteration. Thus their algorithm allows for a very fast iterative erosion process.
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71 ]]>
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72 </help>
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73 <citations>
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74 <citation type="doi">10.1006/cgip.1994.1042</citation>
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75 <citation type="doi">10.1038/nmeth.2102</citation>
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76 </citations>
f6df6830d5ec "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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77 </tool>