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annotate superdsm.xml @ 1:700ae37e5c69 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
author imgteam
date Thu, 06 Jul 2023 00:01:18 +0000
parents 1b0fc671187f
children 244f67290d28
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700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
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1 <tool id="ip_superdsm" name="SuperDSM" version="0.1.3" profile="20.05">
0
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2 <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.3">superdsm</requirement>
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5 <requirement type="package" version="1.6.0">ray-core</requirement>
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6 <requirement type="package" version="0.18.1">scikit-image</requirement>
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7 </requirements>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 python '$__tool_directory__/run-superdsm.py'
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11 '${dataset}'
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12 'cfg.json'
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13 'masks.png'
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14 'overlay.png'
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15 $seg_border
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16 \${GALAXY_SLOTS:-4}
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17 #if str($config.AF_scale) != '':
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18 --AF_scale '${config.AF_scale}'
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19 #end if
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20 #if str($config.c2f_region_analysis_min_atom_radius) != '':
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21 --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
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22 #end if
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23 #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
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24 --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
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25 #end if
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26 #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
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27 --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
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28 #end if
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29 #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
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30 --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
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31 #end if
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32 #if str($config.dsm_alpha) != '':
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33 --dsm_alpha '${config.dsm_alpha}'
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34 #end if
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35 #if str($config.dsm_AF_alpha) != '':
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36 --dsm_AF_alpha '${config.dsm_AF_alpha}'
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37 #end if
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38 #if str($config.global_energy_minimization_beta) != '':
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39 --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
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40 #end if
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41 #if str($config.global_energy_minimization_AF_beta) != '':
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42 --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
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43 #end if
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44 #if str($config.postprocess_mask_max_distance) != '':
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45 --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
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46 #end if
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47 #if str($config.postprocess_mask_stdamp) != '':
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48 --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
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49 #end if
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50 #if str($config.postprocess_max_norm_energy) != '':
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51 --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
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52 #end if
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53 #if str($config.postprocess_min_contrast) != '':
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54 --postprocess_min_contrast '${config.postprocess_min_contrast}'
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55 #end if
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56 #if str($config.postprocess_min_object_radius) != '':
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57 --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
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58 #end if
0
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59 ]]>
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60 </command>
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61 <inputs>
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62 <param name="dataset" type="data" format="tiff,png" label="Dataset" />
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63 <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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64 <section name="config" title="Hyperparameters" expanded="false">
1
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65 <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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66 <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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67 <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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68 <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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69 <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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70 <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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71 <param argument="--dsm_AF_alpha" type="float" value="0.0005" min="0" label="factor used for automatic computation of 𝛼" />
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72 <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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73 <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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74 <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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75 <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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76 <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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77 <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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78 <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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79 </section>
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80 </inputs>
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81 <outputs>
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82 <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" />
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83 <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" />
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84 <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" />
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85 </outputs>
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86 <tests>
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87 <test>
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88 <param name="dataset" value="BBBC033_C2_z28.png" />
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89 <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
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90 </test>
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91 </tests>
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92 <help>
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93 This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.
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94
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95 You can either use an individual input image (PNG, TIF) or a collection of such images.
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96 </help>
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97 <citations>
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98 <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
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99 </citations>
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100 </tool>