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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 18:38:16 +0000
parents 5224cc463a97
children
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4
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
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1 <tool id="ip_threshold" name="Threshold image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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2 <description>with scikit-image</description>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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3 <macros>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
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4 <import>creators.xml</import>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
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5 <import>tests.xml</import>
7d80eb2411fb 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>
7d80eb2411fb 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>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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8 <xml name="inputs/offset">
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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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)." />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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10 </xml>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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11 </macros>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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12 <creator>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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13 <expand macro="creators/bmcv"/>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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14 </creator>
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15 <edam_operations>
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16 <edam_operation>operation_3443</edam_operation>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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17 </edam_operations>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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18 <xrefs>
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19 <xref type="bio.tools">scikit-image</xref>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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20 <xref type="biii">scikit-image</xref>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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21 </xrefs>
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22 <requirements>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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23 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
7d80eb2411fb 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>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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25 </requirements>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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26 <command detect_errors="aggressive">
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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27 <![CDATA[
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28
7d80eb2411fb 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 '$__tool_directory__/auto_threshold.py'
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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30
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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31 '$input'
7d80eb2411fb 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 '$th_method.method_id'
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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35 '$th_method.block_size'
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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36 '$th_method.offset'
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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37 '$th_method.threshold1'
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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38 $invert_output
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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39
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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40 #if str($th_method.threshold2) != '':
7d80eb2411fb 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
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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43
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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44 ]]>
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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45 </command>
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46 <inputs>
3
5224cc463a97 "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" />
4
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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>
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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>
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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" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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62 <param name="block_size" type="hidden" value="0" />
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63 <param name="offset" type="hidden" value="0" />
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64 </when>
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65 <when value="otsu">
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66 <param name="threshold1" type="hidden" value="0" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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67 <param name="threshold2" type="hidden" value="" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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68 <param name="block_size" type="hidden" value="0" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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69 <expand macro="inputs/offset" />
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70 </when>
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71 <when value="li">
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72 <param name="threshold1" type="hidden" value="0" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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73 <param name="threshold2" type="hidden" value="" />
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74 <param name="block_size" type="hidden" value="0" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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75 <expand macro="inputs/offset" />
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76 </when>
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77 <when value="isodata">
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78 <param name="threshold1" type="hidden" value="0" />
7d80eb2411fb 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="" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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80 <param name="block_size" type="hidden" value="0" />
7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
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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>