Mercurial > repos > imgteam > 2d_auto_threshold

annotate auto_threshold.xml @ 9:50fa6150e340 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
author imgteam
date Sat, 07 Jun 2025 18:38:31 +0000
parents 699a5e9146b3
children 2ee04d2ebdcf
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
imgteam
parents: 4
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1 <tool id="ip_threshold" name="Threshold image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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2 <description>with scikit-image</description>
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3 <macros>
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e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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4 <import>creators.xml</import>
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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5 <import>tests.xml</import>
9
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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6 <token name="@TOOL_VERSION@">0.25.0</token>
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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7 <token name="@VERSION_SUFFIX@">0</token>
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e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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8 <xml name="inputs/offset">
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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9 <param name="offset" type="float" value="0" label="Offset" help="Offset to be added to the automatically determined threshold value. Positive values will increase the threshold (and thus reduce the amount of values above the threshold)." />
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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10 </xml>
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7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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11 </macros>
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12 <creator>
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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13 <expand macro="creators/bmcv"/>
e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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14 </creator>
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15 <edam_operations>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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16 <edam_operation>operation_3443</edam_operation>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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17 </edam_operations>
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18 <xrefs>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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19 <xref type="bio.tools">scikit-image</xref>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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20 <xref type="biii">scikit-image</xref>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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21 </xrefs>
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22 <requirements>
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23 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
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50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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24 <requirement type="package" version="0.4.1">giatools</requirement>
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3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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25 </requirements>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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26 <command detect_errors="aggressive">
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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27 <![CDATA[
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50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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29 python '$__tool_directory__/auto_threshold.py'
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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31 '$input'
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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32 ./out.tiff
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33
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34 '$th_method.method_id'
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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35 '$th_method.block_size'
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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36 '$th_method.offset'
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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37 '$th_method.threshold1'
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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38 $invert_output
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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39
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40 #if str($th_method.threshold2) != '':
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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41 --threshold2 '$th_method.threshold2'
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42 #end if
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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43
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44 ]]>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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45 </command>
3df9f0a4bf34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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46 <inputs>
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0c777d708acc "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_auto_threshold/ commit b1b3c63ab021aa77875c3b04127f6836024812f9"
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47 <param name="input" type="data" format="tiff,png" label="Input image" />
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48 <conditional name="th_method">
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49 <param name="method_id" type="select" label="Thresholding method">
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50 <option value="manual">Manual</option>
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51 <option value="otsu" selected="True">Globally adaptive / Otsu</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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52 <option value="li">Globally adaptive / Li's Minimum Cross Entropy</option>
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53 <option value="isodata">Globally adaptive / Isodata</option>
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54 <option value="yen">Globally adaptive / Yen</option>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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55 <option value="loc_gaussian">Locally adaptive / Gaussian</option>
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56 <option value="loc_median">Locally adaptive / Median</option>
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57 <option value="loc_mean">Locally adaptive / Mean</option>
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58 </param>
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59 <when value="manual">
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60 <param name="threshold1" type="float" value="0" label="Threshold value" />
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61 <param name="threshold2" type="float" value="" optional="true" label="Second threshold value for hysteresis thresholding" />
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62 <param name="block_size" type="hidden" value="0" />
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e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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63 <param name="offset" type="hidden" value="0" />
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64 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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65 <when value="otsu">
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66 <param name="threshold1" type="hidden" value="0" />
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67 <param name="threshold2" type="hidden" value="" />
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68 <param name="block_size" type="hidden" value="0" />
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69 <expand macro="inputs/offset" />
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70 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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71 <when value="li">
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72 <param name="threshold1" type="hidden" value="0" />
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73 <param name="threshold2" type="hidden" value="" />
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74 <param name="block_size" type="hidden" value="0" />
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75 <expand macro="inputs/offset" />
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76 </when>
7db4fc31dbee planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 8b9f24cbfaf54f140705f0bf4b6732269bd401da
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77 <when value="isodata">
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78 <param name="threshold1" type="hidden" value="0" />
50fa6150e340 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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79 <param name="threshold2" type="hidden" value="" />
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80 <param name="block_size" type="hidden" value="0" />
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e5c8e7e72373 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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81 <expand macro="inputs/offset" />
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82 </when>
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83 <when value="yen">
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84 <param name="threshold1" type="hidden" value="0" />
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85 <param name="threshold2" type="hidden" value="" />
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86 <param name="block_size" type="hidden" value="0" />
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87 <expand macro="inputs/offset" />
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88 </when>
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89 <when value="loc_gaussian">
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90 <param name="threshold1" type="hidden" value="0" />
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91 <param name="threshold2" type="hidden" value="" />
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92 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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93 <expand macro="inputs/offset" />
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94 </when>
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95 <when value="loc_median">
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96 <param name="threshold1" type="hidden" value="0" />
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97 <param name="threshold2" type="hidden" value="" />
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98 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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99 <expand macro="inputs/offset" />
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100 </when>
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101 <when value="loc_mean">
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102 <param name="threshold1" type="hidden" value="0" />
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103 <param name="threshold2" type="hidden" value="" />
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104 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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105 <expand macro="inputs/offset" />
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106 </when>
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107 </conditional>
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108 <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
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109 </inputs>
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110 <outputs>
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111 <data format="tiff" name="output" from_work_dir="out.tiff" />
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112 </outputs>
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113 <tests>
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114 <!-- Tests for single-channel images (TIFF) -->
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115 <test>
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116 <param name="input" value="sample.tiff"/>
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117 <conditional name="th_method">
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118 <param name="method_id" value="loc_gaussian"/>
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119 <param name="block_size" value="51"/>
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120 </conditional>
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121 <expand macro="tests/binary_image_diff" name="output" value="out1.tiff" ftype="tiff"/>
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122 </test>
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123 <test>
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124 <param name="input" value="sample.tiff"/>
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125 <conditional name="th_method">
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126 <param name="method_id" value="loc_gaussian"/>
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127 <param name="block_size" value="51"/>
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128 <param name="offset" value="1"/>
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129 </conditional>
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130 <expand macro="tests/binary_image_diff" name="output" value="out2.tiff" ftype="tiff"/>
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131 </test>
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132 <test>
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133 <param name="input" value="sample.tiff"/>
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134 <conditional name="th_method">
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135 <param name="method_id" value="otsu"/>
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136 </conditional>
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137 <expand macro="tests/binary_image_diff" name="output" value="out3.tiff" ftype="tiff"/>
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138 </test>
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139 <test>
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140 <param name="input" value="sample.tiff"/>
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141 <param name="invert_output" value="True"/>
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142 <conditional name="th_method">
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143 <param name="method_id" value="manual"/>
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144 <param name="threshold1" value="64"/>
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145 </conditional>
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146 <expand macro="tests/binary_image_diff" name="output" value="out4.tiff" ftype="tiff"/>
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147 </test>
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148 <test>
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149 <param name="input" value="sample.tiff"/>
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150 <conditional name="th_method">
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151 <param name="method_id" value="manual"/>
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152 <param name="threshold1" value="180"/>
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153 <param name="threshold2" value="240"/>
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154 </conditional>
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155 <expand macro="tests/binary_image_diff" name="output" value="sample_manual_180_240.tiff" ftype="tiff"/>
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156 </test>
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157 <!-- Tests for multi-channel images (PNG) -->
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158 <test>
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159 <param name="input" value="rgb.png"/>
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160 <conditional name="th_method">
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161 <param name="method_id" value="otsu"/>
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162 </conditional>
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163 <expand macro="tests/binary_image_diff" name="output" value="rgb_otsu.tiff" ftype="tiff"/>
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164 </test>
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165 <!-- Tests for irregular files -->
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166 <test>
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167 <param name="input" value="sample2.tiff"/>
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168 <conditional name="th_method">
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169 <param name="method_id" value="otsu"/>
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170 </conditional>
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171 <expand macro="tests/binary_image_diff" name="output" value="out5.tiff" ftype="tiff"/>
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172 </test>
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173 </tests>
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174 <help>
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175
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176 **Applies a standard thresholding algorithm to a 2-D single-channel image. Yields a binary image.**
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177
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178 The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used).
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179 The input image is then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold,
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180 and black (pixel value 0) to image regions below or equal to the determined threshold.
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181
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182 The assignment of black and white to image regions below and above the threshold is inverted, if the corresponding option is set.
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183
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184 </help>
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185 <citations>
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186 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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187 </citations>
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188 </tool>