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annotate superdsm.xml @ 4:dc5f72f6b1e9 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
author imgteam
date Mon, 12 Feb 2024 14:58:45 +0000
parents 7fd8dba15bd3
children 9b4830300f3a
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7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>with SuperDSM</description>
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7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.2.0</token>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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5 <token name="@VERSION_SUFFIX@">0</token>
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7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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6 </macros>
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7 <edam_operations>
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8 <edam_operation>operation_3443</edam_operation>
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9 </edam_operations>
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10 <xrefs>
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11 <xref type="bio.tools">superdsm</xref>
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12 <xref type="biii">superdsm</xref>
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13 </xrefs>
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dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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14 <requirements>
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dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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16 <requirement type="package" version="0.2.0">superdsm</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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18 <!--
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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19 Pin the dependencies to specific versions for reproducibility:
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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20 https://github.com/BMCV/SuperDSM#dependency-version-considerations
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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21 -->
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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22 <requirement type="package" version="1.20">numpy</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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23 <requirement type="package" version="1.6.3">scipy</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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24 <requirement type="package" version="0.18.1">scikit-image</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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25 <requirement type="package" version="1.2.6">cvxopt</requirement>
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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26 <requirement type="package" version="1.1.13">cvxpy</requirement>
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27 <requirement type="package" version="1.6.0">ray-core</requirement>
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29 <!--
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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30 2020.0 is the last version of MKL which supports the "MKL_DEBUG_CPU_TYPE" environment variable.
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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31 -->
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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32 <requirement type="package" version="2020.0">mkl</requirement>
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33
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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34 <!--
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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35 Using MKL instead of other BLAS can significantly improve performance on some hardware:
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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36 https://stackoverflow.com/questions/62783262/why-is-numpy-with-ryzen-threadripper-so-much-slower-than-xeon
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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37
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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38 Pinning BLAS to version 1.0 is required for reproducibility:
dc5f72f6b1e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit b0b09d6788778541d1c0b89ca96101fc57d60e22
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39 https://github.com/BMCV/SuperDSM#dependency-version-considerations
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40 -->
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41 <requirement type="package" version="1.0=mkl">blas</requirement>
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42
2
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43 </requirements>
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44 <command detect_errors="aggressive">
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45 <![CDATA[
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46 python '$__tool_directory__/run-superdsm.py'
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47 '${dataset}'
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48 \${GALAXY_SLOTS:-4}
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49 #if 'masks' in $outputs:
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50 --do-masks 'masks.png'
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51 #end if
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52 #if 'cfg' in $outputs:
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53 --do-cfg 'cfg.tsv'
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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54 #end if
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55 #if 'overlay' in $outputs:
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56 --do-overlay 'overlay.png'
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57 #if $seg_border.value % 2 == 1:
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58 #set $seg_border = "%d" % ($seg_border.value + 1)
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59 --do-overlay-border $seg_border
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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60 #else:
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61 --do-overlay-border $seg_border
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62 #end if
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63 #end if
2
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64 #if str($config.AF_scale) != '':
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65 --AF_scale '${config.AF_scale}'
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66 #end if
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67 #if str($config.c2f_region_analysis_min_atom_radius) != '':
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68 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
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69 #end if
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70 #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
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71 --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
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72 #end if
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73 #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
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74 --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
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75 #end if
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76 #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
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77 --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
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78 #end if
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79 #if str($config.dsm_alpha) != '':
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80 --dsm_alpha '${config.dsm_alpha}'
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81 #end if
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82 #if str($config.dsm_AF_alpha) != '':
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83 --dsm_AF_alpha '${config.dsm_AF_alpha}'
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84 #end if
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85 --global_energy_minimization_pruning '${global_energy_minimization_pruning}'
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86 #if str($config.global_energy_minimization_beta) != '':
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87 --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
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88 #end if
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89 #if str($config.global_energy_minimization_AF_beta) != '':
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90 --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
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91 #end if
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92 #if str($config.postprocess_mask_max_distance) != '':
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93 --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
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94 #end if
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95 #if str($config.postprocess_mask_stdamp) != '':
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96 --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
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97 #end if
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98 #if str($config.postprocess_max_norm_energy) != '':
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99 --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
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100 #end if
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101 #if str($config.postprocess_min_contrast) != '':
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102 --postprocess_min_contrast '${config.postprocess_min_contrast}'
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103 #end if
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104 #if str($config.postprocess_min_object_radius) != '':
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105 --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
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106 #end if
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107 ]]>
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108 </command>
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109 <environment_variables>
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110
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111 <!--
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112 This enables accelerated CPU instruction sets on AMD hardware, does nothing in Intel hardware, thus no need to change this:
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113 -->
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114 <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable>
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115
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116 </environment_variables>
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117 <inputs>
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118 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
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119 <param argument="--global_energy_minimization_pruning" type="select" label="Graph pruning for global energy minimization" help="Exact graph pruning corresponds to the original algorithm, which provably yields globally optimal results. Robust graph pruning is more greedy and has a provably bounded approximation error. Depending on the data, this can be significantly faster than exact graph pruning, without degrading the segmentation or cluster splitting performance.">
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120 <option value="exact">Exact graph pruning (Kostrykin and Rohr, TPAMI 2023)</option>
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121 <option value="isbi24" selected="true">Robust graph pruning (Kostrykin and Rohr, ISBI 2024)</option>
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122 </param>
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123 <param name="outputs" type="select" label="Tool outputs" multiple="true" optional="false" help="Note that if neither a segmentation overlay nor a label map is created, segmentation and cluster splitting will not be performed. As a consequence, hyperparameters which are determined automatically during segmentation and cluster splitting will not be reported, even if &quot;Report all hyperparameters&quot; is selected.">
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124 <option value="overlay" selected="true">Create a segmentation overlay</option>
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125 <option value="masks">Create a label map (e.g., for further processing)</option>
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126 <option value="cfg">Report all hyperparameters (manually set and automatically determined values)</option>
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127 </param>
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128 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels)" help="This parameter is only used for segmentation overlays (see above)." />
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129 <section name="config" title="Hyperparameters" expanded="false">
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130 <param argument="--AF_scale" optional="true" type="float" value="" min="0" label="scale Οƒ" help="The scale of the objects to be segmented. Leave empty to use the automatically determined value." />
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131 <param argument="--c2f_region_analysis_min_atom_radius" optional="true" type="float" value="" min="0" label="min_atom_radius" help="No region determined by the Coarse-to-fine region analysis scheme is smaller than a circle of this radius (in terms of the surface area). Leave empty to use the automatically determined value." />
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132 <param argument="--c2f_region_analysis_min_norm_energy_improvement" type="float" value="0.1" min="0" label="min_norm_energy_improvement" help="Each split performed during the computation of the atomic image regions must improve the normalized energy π‘Ÿ(πœ”) of an image region πœ” by at least this factor. Given that an image region is split into the sub-regions πœ”β‚, πœ”β‚‚, the improvement of the split is defined by the fraction max{π‘Ÿ(πœ”)₁, π‘Ÿ(πœ”β‚‚)} / π‘Ÿ(πœ”β‚ βˆͺ πœ”β‚‚). Lower values of the fraction correspond to better improvements." />
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133 <param argument="--c2f_region_analysis_max_atom_norm_energy" type="float" value="0.05" min="0" label="max_norm_energy1" help="No atomic image region πœ” determined by the Coarse-to-fine region analysis has a normalized energy π‘Ÿ(πœ”) smaller than this value." />
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134 <param argument="--c2f_region_analysis_max_cluster_marker_irregularity" type="float" value="0.2" min="0" label="max_pa_ratio" help="Threshold for the β€œirregularity” of image regions. Image regions with an β€œirregularity” higher than this value are masked as β€œempty” image regions and discarded from further considerations." />
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135 <param argument="--dsm_alpha" type="float" value="" optional="true" min="0" label="regularization of the deformations 𝛼" help="Governs the regularization of the deformations. Increasing this value leads to a smoother segmentation result. Leave empty to use the automatically determined value." />
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136 <param argument="--dsm_AF_alpha" type="float" value="0.0005" min="0" label="factor used for automatic computation of 𝛼" />
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137 <param argument="--global_energy_minimization_beta" type="float" value="" optional="true" min="0" label="sparsity 𝛽" help="Increasing this value leads to a sparser segmentation result. Leave empty to use the automatically determined value." />
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138 <param argument="--global_energy_minimization_AF_beta" type="float" value="0.66" min="0" label="factor used for automatic computation of 𝛽" />
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139 <param argument="--postprocess_mask_max_distance" type="integer" value="1" min="0" label="mask_max_distance" help="Image points within this maximum distance of the boundary of the original segmentation mask are subject to refinement in post-processing. Image points further away from the boundary are neither added to nor removed from the segmentation mask." />
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140 <param argument="--postprocess_mask_stdamp" type="float" value="2" min="0" label="mask_stdamp" help="An image point adjacent to the boundary of the original segmentation mask is added to the segmentation mask in post-processing, if its Gaussian-smoothed intensity is sufficiently similar to the mean intensity of the mask. The image point is removed otherwise. The lower the value set, the stricter the similarity must be." />
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141 <param argument="--postprocess_max_norm_energy" type="float" value="0.2" label="max_norm_energy2" help="Objects with a normalized energy larger than this value are discarded in post-processing." />
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142 <param argument="--postprocess_min_contrast" type="float" value="1.35" label="min_contrast" help="A segmented object is discarded in post-processing, if the contrast as defined above is below this threshold." />
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143 <param argument="--postprocess_min_object_radius" type="float" value="0" label="min_object_radius" help="Objects smaller than a circle of this radius are discarded in post-processing (in terms of the surface area)." />
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144 </section>
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145 </inputs>
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146 <outputs>
3
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147 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks">
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148 <filter>'masks' in outputs</filter>
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149 </data>
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150 <data format="tsv" name="cfg" from_work_dir="cfg.tsv" label="${tool.name} on ${on_string}: cfg">
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151 <filter>'cfg' in outputs</filter>
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152 </data>
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153 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay">
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154 <filter>'overlay' in outputs</filter>
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155 </data>
0
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156 </outputs>
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157 <tests>
3
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158 <test expect_num_outputs="3">
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159 <param name="dataset" value="BBBC033_C2_z28.png" />
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160 <param name="global_energy_minimization_pruning" value="exact" />
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161 <param name="outputs" value="overlay,masks,cfg" />
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162 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
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163 <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" />
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164 </test>
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165 <test expect_num_outputs="1">
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166 <param name="dataset" value="BBBC033_C2_z28.png" />
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167 <param name="global_energy_minimization_pruning" value="exact" />
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168 <param name="outputs" value="cfg" />
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169 <output name="cfg" value="cfg.tsv" ftype="tsv" compare="diff" />
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170 </test>
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171 </tests>
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172 <help>
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173 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
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174
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175 You can either use an individual input image (PNG, TIF) or a collection of such images.
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176 </help>
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177 <citations>
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178 <citation type="bibtex">
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179 @inproceedings{kostrykin2024,
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180 author = {Kostrykin, L. and Rohr, K.},
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181 title = {Robust Graph Pruning for Efficient Segmentation and Cluster Splitting of Cell Nuclei using Deformable Shape Models},
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182 booktitle = {Proc. IEEE International Symposium on Biomedical Imaging (ISBI'24)},
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183 pages = {accepted for presentation},
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184 year = {2024},
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185 }
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186 </citation>
0
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187 <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
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188 </citations>
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189 </tool>