Mercurial > repos > iuc > imagej2_analyze_particles_binary

annotate imagej2_macros.xml @ 0:d065ec177dcd draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:36:17 -0400
parents
children dd9041dc3c27
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <macros>
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3 <token name="@WRAPPER_VERSION@">1.0</token>
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4 <xml name="fiji_requirements">
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5 <requirements>
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6 <requirement type="package" version="20141125">fiji</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="python_bioformats_requirements">
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10 <requirements>
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11 <requirement type="package" version="20141125">fiji</requirement>
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12 <requirement type="package" version="1.0.11">javabridge</requirement>
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13 <requirement type="package" version="1.9">numpy</requirement>
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14 <requirement type="package" version="1.0.4">python_bioformats</requirement>
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15 </requirements>
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16 </xml>
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17 <xml name="stdio">
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18 <stdio>
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19 <exit_code range="1:"/>
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20 <exit_code range=":-1"/>
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21 <regex match="Error:"/>
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22 <regex match="Exception:"/>
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23 </stdio>
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24 </xml>
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25 <xml name="image_type">
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26 <param name="image_type" type="select" label="Image type">
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27 <option value="8-bit_white" selected="True">8-bit white</option>
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28 <option value="8-bit_black">8-bit black</option>
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29 <option value="8-bit_random">8-bit random</option>
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30 <option value="8-bit_ramp">8-bit ramp</option>
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31 <option value="16-bit_white">16-bit white</option>
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32 <option value="16-bit_black">16-bit black</option>
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33 <option value="16-bit_random">16-bit random</option>
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34 <option value="16-bit_ramp">16-bit ramp</option>
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35 <option value="32-bit_white">32-bit white</option>
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36 <option value="32-bit_black">32-bit black</option>
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37 <option value="32-bit_random">32-bit random</option>
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38 <option value="32-bit_ramp">32-bit ramp</option>
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39 <option value="RGB_white">RGB white</option>
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40 <option value="RGB_black">RGB black</option>
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41 <option value="RGB_random">RGB random</option>
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42 <option value="RGB_ramp">RGB ramp</option>
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43 </param>
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44 </xml>
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45 <xml name="make_binary_params">
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46 <param name="iterations" type="integer" value="1" min="1" max="100" label="Iterations" help="The number of times (1-100) erosion, dilation, opening, and closing are performed."/>
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47 <param name="count" type="integer" value="1" min="1" max="8" label="Count" help="The number of adjacent background pixels necessary (1-8) for erosion or dilation."/>
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48 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
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49 <option value="no" selected="True">No</option>
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50 <option value="yes">Yes</option>
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51 </param>
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52 <param name="pad_edges_when_eroding" type="select" label="Pad edges when eroding" help="If Yes, eroding does not erode from the edges of the image.">
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53 <option value="no" selected="True">No</option>
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54 <option value="yes">Yes</option>
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55 </param>
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56 </xml>
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57 <xml name="black_background_param">
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58 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
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59 <option value="no" selected="True">No</option>
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60 <option value="yes">Yes</option>
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61 </param>
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62 </xml>
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63 <token name="@make_binary_args@">
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64 --iterations $iterations
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65 --count $count
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66 --black_background $black_background
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67 --pad_edges_when_eroding $pad_edges_when_eroding
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68 </token>
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69 <token name="@requires_binary_input@">
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70 .. class:: warningmark
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71
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72 This tool works on binary images, so other image types will automatically be converted to binary
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73 before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with
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74 the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool
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75 allows you to choose the **Black background** setting. If these settings are not appropriate,
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76 first manually convert the image to binary using the **Convert to binary (black and white) with ImageJ2**
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77 tool, which allows you to change them.
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78 </token>
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79 <xml name="image_datatypes">
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80 <option value="bmp">bmp</option>
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81 <option value="gif">gif</option>
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82 <option value="jpg">jpg</option>
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83 <option value="png" selected="true">png</option>
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84 <option value="tiff">tiff</option>
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85 </xml>
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86 <xml name="bunwarpj_citations">
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87 <citations>
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88 <citation type="bibtex">
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89 @InProceedings(Arganda-Carreras2006,
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90 author = "Ignacio Arganda-Carreras and
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91 Carlos Oscar S{\'a}nchez Sorzano and
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92 Roberto Marabini and
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93 Jos{\'e} Mar\'{\i}a Carazo and
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94 Carlos Ortiz-de-Solorzano and
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95 Jan Kybic",
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96 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",
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97 publisher = "Springer Berlin / Heidelberg",
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98 booktitle = "Computer Vision Approaches to Medical Image Analysis",
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99 series = "Lecture Notes in Computer Science",
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100 year = "2006",
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101 volume = "4241",
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102 pages = "85-95",
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103 month = "May",
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104 city = "Graz, Austria")
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105 </citation>
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106 <citation type="doi">10.1038/nmeth.2019</citation>
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107 </citations>
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108 </xml>
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109 <xml name="fiji_headless_citations">
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110 <citations>
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111 <citation type="doi">10.1038/nmeth.2102</citation>
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112 </citations>
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113 </xml>
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114 <xml name="bioformats_fiji_javabridge_citations">
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115 <citations>
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116 <citation type="doi">10.1038/nmeth.2102</citation>
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117 <citation type="doi">10.1038/nmeth.2019</citation>
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118 <citation type="doi">10.1083/jcb.201004104</citation>
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119 </citations>
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120 </xml>
d065ec177dcd planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
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121 </macros>