Mercurial > repos > imgteam > superdsm
diff superdsm.xml @ 2:7fcd96cf0d52 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 597cb3dc531963d02c5db0e4fc2596fcb06728dd
| author | imgteam |
|---|---|
| date | Wed, 17 Dec 2025 22:28:28 +0000 |
| parents | 680b866ba043 |
| children | c2412cb5fc2e |
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--- a/superdsm.xml Thu Jul 06 00:01:07 2023 +0000 +++ b/superdsm.xml Wed Dec 17 22:28:28 2025 +0000 @@ -1,66 +1,137 @@ -<tool id="ip_superdsm" name="SuperDSM" version="0.1.3" profile="20.05"> - <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description> - <requirements> - <requirement type="package" version="0.1.3">superdsm</requirement> - <requirement type="package" version="1.6.0">ray-core</requirement> +<tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description>with SuperDSM</description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + <token name="@TOOL_VERSION@">0.2.0</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> + <creator> + <expand macro="creators/bmcv"/> + </creator> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">superdsm</xref> + <xref type="biii">superdsm</xref> + </xrefs> + <requirements> + + <requirement type="package" version="@TOOL_VERSION@">superdsm</requirement> + <requirement type="package" version="0.1.1">giatools</requirement> + + <!-- + Pin the dependencies to specific versions for reproducibility: + https://github.com/BMCV/SuperDSM#dependency-version-considerations + --> + <requirement type="package" version="1.20">numpy</requirement> + <requirement type="package" version="1.6.3">scipy</requirement> <requirement type="package" version="0.18.1">scikit-image</requirement> - </requirements> - <command detect_errors="aggressive"> - <![CDATA[ - python '$__tool_directory__/run-superdsm.py' - '${dataset}' - 'cfg.json' - 'masks.png' - 'overlay.png' - $seg_border - \${GALAXY_SLOTS:-4} - #if str($config.AF_scale) != '': - --AF_scale '${config.AF_scale}' - #end if - #if str($config.c2f_region_analysis_min_atom_radius) != '': - --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}' - #end if - #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '': - --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}' - #end if - #if str($config.c2f_region_analysis_max_atom_norm_energy) != '': - --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}' - #end if - #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '': - --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}' - #end if - #if str($config.dsm_alpha) != '': - --dsm_alpha '${config.dsm_alpha}' - #end if - #if str($config.dsm_AF_alpha) != '': - --dsm_AF_alpha '${config.dsm_AF_alpha}' - #end if - #if str($config.global_energy_minimization_beta) != '': - --global_energy_minimization_beta '${config.global_energy_minimization_beta}' - #end if - #if str($config.global_energy_minimization_AF_beta) != '': - --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}' - #end if - #if str($config.postprocess_mask_max_distance) != '': - --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}' - #end if - #if str($config.postprocess_mask_stdamp) != '': - --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}' - #end if - #if str($config.postprocess_max_norm_energy) != '': - --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}' - #end if - #if str($config.postprocess_min_contrast) != '': - --postprocess_min_contrast '${config.postprocess_min_contrast}' - #end if - #if str($config.postprocess_min_object_radius) != '': - --postprocess_min_object_radius '${config.postprocess_min_object_radius}' - #end if - ]]> - </command> - <inputs> + <requirement type="package" version="1.2.6">cvxopt</requirement> + <requirement type="package" version="1.1.13">cvxpy</requirement> + <requirement type="package" version="1.6.0">ray-core</requirement> + + <!-- + 2020.0 is the last version of MKL which supports the "MKL_DEBUG_CPU_TYPE" environment variable. + --> + <requirement type="package" version="2020.0">mkl</requirement> + + <!-- + Using MKL instead of other BLAS can significantly improve performance on some hardware: + https://stackoverflow.com/questions/62783262/why-is-numpy-with-ryzen-threadripper-so-much-slower-than-xeon + + Pinning BLAS to version 1.0 is required for reproducibility: + https://github.com/BMCV/SuperDSM#dependency-version-considerations + --> + <requirement type="package" version="1.0=mkl">blas</requirement> + + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python '$__tool_directory__/run-superdsm.py' + '${dataset}' + \${GALAXY_SLOTS:-4} + #if 'masks' in $outputs: + --do-masks 'masks.png' + #end if + #if 'cfg' in $outputs: + --do-cfg 'cfg.tsv' + #end if + #if 'overlay' in $outputs: + --do-overlay 'overlay.png' + #if $seg_border.value % 2 == 1: + #set $seg_border = "%d" % ($seg_border.value + 1) + --do-overlay-border $seg_border + #else: + --do-overlay-border $seg_border + #end if + #end if + #if str($config.AF_scale) != '': + --AF_scale '${config.AF_scale}' + #end if + #if str($config.c2f_region_analysis_min_atom_radius) != '': + --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}' + #end if + #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '': + --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}' + #end if + #if str($config.c2f_region_analysis_max_atom_norm_energy) != '': + --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}' + #end if + #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '': + --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}' + #end if + #if str($config.dsm_alpha) != '': + --dsm_alpha '${config.dsm_alpha}' + #end if + #if str($config.dsm_AF_alpha) != '': + --dsm_AF_alpha '${config.dsm_AF_alpha}' + #end if + --global_energy_minimization_pruning '${global_energy_minimization_pruning}' + #if str($config.global_energy_minimization_beta) != '': + --global_energy_minimization_beta '${config.global_energy_minimization_beta}' + #end if + #if str($config.global_energy_minimization_AF_beta) != '': + --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}' + #end if + #if str($config.postprocess_mask_max_distance) != '': + --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}' + #end if + #if str($config.postprocess_mask_stdamp) != '': + --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}' + #end if + #if str($config.postprocess_max_norm_energy) != '': + --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}' + #end if + #if str($config.postprocess_min_contrast) != '': + --postprocess_min_contrast '${config.postprocess_min_contrast}' + #end if + #if str($config.postprocess_min_object_radius) != '': + --postprocess_min_object_radius '${config.postprocess_min_object_radius}' + #end if + ]]> + </command> + <environment_variables> + + <!-- + This enables accelerated CPU instruction sets on AMD hardware, does nothing in Intel hardware, thus no need to change this: + --> + <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable> + + </environment_variables> + <inputs> <param name="dataset" type="data" format="tiff,png" label="Dataset" /> - <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" /> + <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."> + <option value="exact">Exact graph pruning (Kostrykin and Rohr, TPAMI 2023)</option> + <option value="isbi24" selected="true">Robust graph pruning (Kostrykin and Rohr, ISBI 2024)</option> + </param> + <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 "Report all hyperparameters" is selected."> + <option value="overlay" selected="true">Create a segmentation overlay</option> + <option value="masks">Create a label map (e.g., for further processing)</option> + <option value="cfg">Report all hyperparameters (manually set and automatically determined values)</option> + </param> + <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)." /> <section name="config" title="Hyperparameters" expanded="false"> <param argument="--AF_scale" optional="true" type="float" value="" min="0" label="scale σ" help="The scale of the objects to be segmented. Leave empty to use the automatically determined value." /> <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." /> @@ -79,22 +150,60 @@ </section> </inputs> <outputs> - <data format="json" name="cfg" from_work_dir="cfg.json" label="${tool.name} on ${on_string}: cfg" /> - <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks" /> - <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay" /> + <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks"> + <filter>'masks' in outputs</filter> + </data> + <data format="tsv" name="cfg" from_work_dir="cfg.tsv" label="${tool.name} on ${on_string}: cfg"> + <filter>'cfg' in outputs</filter> + </data> + <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay"> + <filter>'overlay' in outputs</filter> + </data> </outputs> <tests> - <test> + <test expect_num_outputs="3"> <param name="dataset" value="BBBC033_C2_z28.png" /> - <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" /> + <param name="global_energy_minimization_pruning" value="exact" /> + <param name="outputs" value="overlay,masks,cfg" /> + <expand macro="tests/intensity_image_diff" name="overlay" value="overlay.png" ftype="png"/> + <output name="cfg" value="cfg-full.tsv" ftype="tsv" compare="diff" /> + <output name="masks" ftype="png"> + <assert_contents> + + <has_image_width width="1024"/> + <has_image_height height="1344"/> + <has_image_channels channels="1"/> + <has_image_n_labels n="16"/><!-- 15 objects plus the background --> + + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="dataset" value="BBBC033_C2_z28.png" /> + <param name="global_energy_minimization_pruning" value="exact" /> + <param name="outputs" value="cfg" /> + <output name="cfg" value="cfg.tsv" ftype="tsv" compare="diff" /> </test> </tests> <help> - This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images. + + **Performs segmentation of 2-D fluorescence microscopy images using deformable shape models and superadditivity.** - You can either use an individual input image (PNG, TIF) or a collection of such images. + SuperDSM is a globally optimal method for cell nuclei segmentation using deformable shape models and their inherent law of superadditivity. + + You can either use an individual input image (PNG, TIFF) or a collection of such images. + </help> <citations> + <citation type="bibtex"> + @inproceedings{kostrykin2024, + author = {Kostrykin, L. and Rohr, K.}, + title = {Robust Graph Pruning for Efficient Segmentation and Cluster Splitting of Cell Nuclei using Deformable Shape Models}, + booktitle = {Proc. IEEE International Symposium on Biomedical Imaging (ISBI'24)}, + pages = {accepted for presentation}, + year = {2024}, + } + </citation> <citation type="doi">10.1109/TPAMI.2022.3185583</citation> </citations> </tool>