Mercurial > repos > imgteam > 2d_auto_threshold

annotate auto_threshold.xml @ 5:1ae14e703e5b 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 14:42:51 +0000
parents 7d80eb2411fb
children
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7d80eb2411fb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
imgteam
parents: 3
diff changeset
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
imgteam
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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
imgteam
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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>
5
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
imgteam
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6 <token name="@TOOL_VERSION@">0.25.2</token>
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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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
imgteam
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8 <xml name="inputs/offset">
5
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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9 <param name="offset" type="float" value="0" label="Offset"
1ae14e703e5b 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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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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11 </xml>
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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12 </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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13 <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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14 <expand macro="creators/bmcv"/>
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15 <expand macro="creators/kostrykin"/>
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16 </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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17 <edam_operations>
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18 <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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19 </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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20 <xrefs>
5
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21 <xref type="bio.tools">galaxy_image_analysis</xref>
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22 <xref type="bio.tools">giatools</xref>
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23 <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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24 <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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25 </xrefs>
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 <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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27 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
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1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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28 <requirement type="package" version="0.7.3">giatools</requirement>
1ae14e703e5b 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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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 </requirements>
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31 <required_files>
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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32 <include type="literal" path="auto_threshold.py"/>
1ae14e703e5b 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>
1ae14e703e5b 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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35
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 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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37
5
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38 #if $input.extension == "zarr"
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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39 --input '$input.extra_files_path/$input.metadata.store_root'
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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40 #else
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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41 --input '$input'
4
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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
5
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44 --output ./out.tiff
1ae14e703e5b 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 '$params'
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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46 --verbose
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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47
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48 ]]></command>
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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49 <configfiles>
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50 <configfile name="params"><![CDATA[
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51 {
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52
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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53 #if str($th_method.method_id).startswith('loc_')
1ae14e703e5b 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"
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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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": $th_method.threshold2,
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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64 #else
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65 "threshold2": null,
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66 #end if
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67
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68 #end if
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69
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70 "method": "$th_method.method_id",
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71 "invert": $invert_output
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72
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73 }
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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74 ]]></configfile>
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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75 </configfiles>
4
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76 <inputs>
5
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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">
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 <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>