Mercurial > repos > imgteam > 2d_auto_threshold

annotate auto_threshold.xml @ 10:2ee04d2ebdcf draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
author imgteam
date Sat, 03 Jan 2026 14:43:10 +0000
parents 50fa6150e340
children
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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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1 <tool id="ip_threshold" name="Threshold image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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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>
10
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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6 <token name="@TOOL_VERSION@">0.25.2</token>
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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">
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9 <param name="offset" type="float" value="0" label="Offset"
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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10 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)."/>
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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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11 </xml>
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12 </macros>
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13 <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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14 <expand macro="creators/bmcv"/>
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15 <expand macro="creators/kostrykin"/>
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16 </creator>
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17 <edam_operations>
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18 <edam_operation>operation_3443</edam_operation>
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19 </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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20 <xrefs>
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21 <xref type="bio.tools">galaxy_image_analysis</xref>
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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22 <xref type="bio.tools">giatools</xref>
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23 <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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24 <xref type="biii">scikit-image</xref>
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25 </xrefs>
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26 <requirements>
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27 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
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28 <requirement type="package" version="0.7.3">giatools</requirement>
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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29 <requirement type="package" version="0.12.2">ome-zarr</requirement>
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30 </requirements>
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31 <required_files>
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32 <include type="literal" path="auto_threshold.py"/>
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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33 </required_files>
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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34 <command detect_errors="aggressive"><![CDATA[
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36 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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37
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38 #if $input.extension == "zarr"
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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39 --input '$input.extra_files_path/$input.metadata.store_root'
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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40 #else
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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41 --input '$input'
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42 #end if
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43
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44 --output ./out.tiff
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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45 --params '$params'
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46 --verbose
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47
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48 ]]></command>
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49 <configfiles>
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50 <configfile name="params"><![CDATA[
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51 {
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52
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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53 #if str($th_method.method_id).startswith('loc_')
2ee04d2ebdcf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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54 "block_size": $th_method.block_size,
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55 #end if
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56
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57 #if $th_method.method_id != "manual"
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58 "offset": $th_method.offset,
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59
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60 #else
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61 "threshold1": $th_method.threshold1,
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62 #if str($th_method.threshold2) != ""
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63 "threshold2": $th_method.threshold2,
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64 #else
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65 "threshold2": null,
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66 #end if
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67
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68 #end if
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69
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70 "method": "$th_method.method_id",
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71 "invert": $invert_output
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72
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73 }
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74 ]]></configfile>
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75 </configfiles>
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76 <inputs>
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77 <param name="input" type="data" format="tiff,zarr,png,jpg" label="Input image"/>
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78 <conditional name="th_method">
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79 <param name="method_id" type="select" label="Thresholding method">
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80 <option value="manual">Manual</option>
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81 <option value="otsu" selected="True">Globally adaptive / Otsu</option>
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82 <option value="li">Globally adaptive / Li's Minimum Cross Entropy</option>
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83 <option value="isodata">Globally adaptive / Isodata</option>
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84 <option value="yen">Globally adaptive / Yen</option>
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85 <option value="loc_gaussian">Locally adaptive / Gaussian</option>
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86 <option value="loc_median">Locally adaptive / Median</option>
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87 <option value="loc_mean">Locally adaptive / Mean</option>
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88 </param>
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89 <when value="manual">
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90 <param name="threshold1" type="float" value="0" label="Threshold value"/>
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91 <param name="threshold2" type="float" value="" optional="true" label="Second threshold value for hysteresis thresholding"/>
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92 <param name="offset" type="hidden" value="0"/>
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93 </when>
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94 <when value="otsu">
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95 <expand macro="inputs/offset"/>
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96 </when>
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97 <when value="li">
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98 <expand macro="inputs/offset"/>
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99 </when>
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100 <when value="isodata">
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101 <expand macro="inputs/offset"/>
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102 </when>
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103 <when value="yen">
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104 <expand macro="inputs/offset"/>
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105 </when>
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106 <when value="loc_gaussian">
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107 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold"/>
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108 <expand macro="inputs/offset"/>
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109 </when>
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110 <when value="loc_median">
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111 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold"/>
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112 <expand macro="inputs/offset"/>
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113 </when>
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114 <when value="loc_mean">
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115 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold"/>
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116 <expand macro="inputs/offset"/>
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117 </when>
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118 </conditional>
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119 <param name="invert_output" type="boolean" checked="false" label="Invert output labels"
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120 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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121 </inputs>
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122 <outputs>
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123 <data format="tiff" name="output" from_work_dir="out.tiff" />
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124 </outputs>
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125 <tests>
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126 <!-- Tests for single-channel images (TIFF) -->
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127 <test>
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128 <param name="input" value="input/sample.tiff"/>
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129 <conditional name="th_method">
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130 <param name="method_id" value="loc_gaussian"/>
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131 <param name="block_size" value="51"/>
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132 </conditional>
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133 <expand macro="tests/binary_image_diff" name="output" value="output/out1.tiff" ftype="tiff"/>
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134 </test>
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135 <test>
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136 <param name="input" value="input/sample.tiff"/>
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137 <conditional name="th_method">
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138 <param name="method_id" value="loc_gaussian"/>
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139 <param name="block_size" value="51"/>
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140 <param name="offset" value="1"/>
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141 </conditional>
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142 <expand macro="tests/binary_image_diff" name="output" value="output/out2.tiff" ftype="tiff"/>
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143 </test>
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144 <test>
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145 <param name="input" value="input/sample.tiff"/>
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146 <conditional name="th_method">
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147 <param name="method_id" value="otsu"/>
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148 </conditional>
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149 <expand macro="tests/binary_image_diff" name="output" value="output/out3.tiff" ftype="tiff"/>
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150 </test>
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151 <test>
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152 <param name="input" value="input/sample.tiff"/>
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153 <param name="invert_output" value="True"/>
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154 <conditional name="th_method">
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155 <param name="method_id" value="manual"/>
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156 <param name="threshold1" value="64"/>
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157 </conditional>
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158 <expand macro="tests/binary_image_diff" name="output" value="output/out4.tiff" ftype="tiff"/>
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159 </test>
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160 <test>
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161 <param name="input" value="input/sample.tiff"/>
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162 <conditional name="th_method">
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163 <param name="method_id" value="manual"/>
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164 <param name="threshold1" value="180"/>
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165 <param name="threshold2" value="240"/>
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166 </conditional>
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167 <expand macro="tests/binary_image_diff" name="output" value="output/sample_manual_180_240.tiff" ftype="tiff"/>
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168 </test>
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169 <!-- Tests for multi-channel images (PNG) -->
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170 <test>
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171 <param name="input" value="input/rgb.png"/>
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172 <conditional name="th_method">
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173 <param name="method_id" value="otsu"/>
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174 </conditional>
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175 <expand macro="tests/binary_image_diff" name="output" value="output/rgb_otsu.tiff" ftype="tiff"/>
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176 </test>
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177 <!-- Tests for irregular files (TODO: clear up what this means) -->
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178 <test>
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179 <param name="input" value="input/sample2.tiff"/>
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180 <conditional name="th_method">
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181 <param name="method_id" value="otsu"/>
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182 </conditional>
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183 <expand macro="tests/binary_image_diff" name="output" value="output/out5.tiff" ftype="tiff"/>
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184 </test>
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185 <!-- Tests for exotic files -->
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186 <test>
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187 <param name="input" value="input/input5.jpg"/>
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188 <conditional name="th_method">
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189 <param name="method_id" value="li"/>
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190 </conditional>
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191 <expand macro="tests/binary_image_diff" name="output" value="output/input5_li.tiff" ftype="tiff"/>
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192 </test>
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193 <test>
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194 <param name="input" value="input/input8_zyx.zarr"/>
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195 <conditional name="th_method">
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196 <param name="method_id" value="yen"/>
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197 </conditional>
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198 <expand macro="tests/binary_image_diff" name="output" value="output/input8_yen.tiff" ftype="tiff"/>
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199 </test>
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200 </tests>
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201 <help>
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202
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203 **Applies a standard thresholding algorithm to an image. Yields a binary image.**
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204
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205 The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used). The input image is
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206 then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold, and black (pixel value 0)
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207 to image regions below or equal to the determined threshold. For multi-channel images, each channel is processed separately,
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208 which, for example, may also yield colors beyond black and white in case of RGB images.
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209
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210 The assignment of the pixel values 0 and 255 (i.e. black and white) to image regions below and above the threshold is inverted,
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211 if the corresponding option is set.
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212
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213 </help>
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214 <citations>
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215 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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216 </citations>
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217 </tool>