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annotate superdsm.xml @ 2:244f67290d28 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:35 +0000
parents 700ae37e5c69
children 7fd8dba15bd3
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244f67290d28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="0.1.3+galaxy2" profile="20.05">
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2 <description>with SuperDSM</description>
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3 <edam_operations>
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4 <edam_operation>operation_3443</edam_operation>
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5 </edam_operations>
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6 <xrefs>
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7 <xref type="bio.tools">superdsm</xref>
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8 <xref type="biii">superdsm</xref>
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9 </xrefs>
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10 <requirements>
1
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11 <requirement type="package" version="0.1.3">superdsm</requirement>
0
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12 <requirement type="package" version="1.6.0">ray-core</requirement>
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13 <requirement type="package" version="0.18.1">scikit-image</requirement>
2
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14 <requirement type="package" version="2020.0">mkl</requirement><!-- this seems to be the last version of MKL which supports the "MKL_DEBUG_CPU_TYPE" environment variable -->
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15 <requirement type="package" version="*=mkl">blas</requirement><!-- using MKL instead of other BLAS can significantly improve performance on some hardware, cf. https://stackoverflow.com/questions/62783262/why-is-numpy-with-ryzen-threadripper-so-much-slower-than-xeon -->
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16 </requirements>
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17 <command detect_errors="aggressive">
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18 <![CDATA[
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19 python '$__tool_directory__/run-superdsm.py'
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20 '${dataset}'
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21 'cfg.json'
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22 'masks.png'
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23 'overlay.png'
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24 $seg_border
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25 \${GALAXY_SLOTS:-4}
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26 #if str($config.AF_scale) != '':
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27 --AF_scale '${config.AF_scale}'
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28 #end if
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29 #if str($config.c2f_region_analysis_min_atom_radius) != '':
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30 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
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31 #end if
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32 #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
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33 --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
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34 #end if
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35 #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
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36 --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
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37 #end if
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38 #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
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39 --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
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40 #end if
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41 #if str($config.dsm_alpha) != '':
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42 --dsm_alpha '${config.dsm_alpha}'
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43 #end if
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44 #if str($config.dsm_AF_alpha) != '':
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45 --dsm_AF_alpha '${config.dsm_AF_alpha}'
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46 #end if
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47 #if str($config.global_energy_minimization_beta) != '':
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48 --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
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49 #end if
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50 #if str($config.global_energy_minimization_AF_beta) != '':
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51 --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
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52 #end if
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53 #if str($config.postprocess_mask_max_distance) != '':
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54 --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
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55 #end if
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56 #if str($config.postprocess_mask_stdamp) != '':
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57 --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
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58 #end if
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59 #if str($config.postprocess_max_norm_energy) != '':
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60 --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
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61 #end if
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62 #if str($config.postprocess_min_contrast) != '':
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63 --postprocess_min_contrast '${config.postprocess_min_contrast}'
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64 #end if
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65 #if str($config.postprocess_min_object_radius) != '':
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66 --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
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67 #end if
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68 ]]>
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69 </command>
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70 <environment_variables>
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71 <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable><!-- this enables accelerated CPU instruction sets on AMD hardware, does nothing in Intel hardware, thus no need to change this -->
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72 </environment_variables>
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73 <inputs>
0
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74 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
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75 <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" />
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76 <section name="config" title="Hyperparameters" expanded="false">
1
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77 <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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78 <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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79 <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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80 <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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81 <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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82 <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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83 <param argument="--dsm_AF_alpha" type="float" value="0.0005" min="0" label="factor used for automatic computation of 𝛼" />
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84 <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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85 <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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86 <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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87 <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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88 <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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89 <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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90 <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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91 </section>
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92 </inputs>
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93 <outputs>
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94 <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" />
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95 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" />
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96 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" />
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="dataset" value="BBBC033_C2_z28.png" />
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101 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
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102 </test>
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103 </tests>
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104 <help>
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105 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
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106
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107 You can either use an individual input image (PNG, TIF) or a collection of such images.
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108 </help>
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109 <citations>
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110 <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
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111 </citations>
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112 </tool>