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@paulzierep
paulzierep committed Jun 3, 2024
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142 changes: 75 additions & 67 deletions results/all_tools.tsv
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33 changes: 31 additions & 2 deletions results/imaging/index.html
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<td>bgruening</td>
<td>https://github.com/bgruening/galaxytools/tree/master/tools/cellpose</td>
<td>https://github.com/bgruening/galaxytools/tree/master/tools/cellpose</td>
<td>3.0.1</td>
<td></td>
<td>3.0.8</td>
<td>cellpose</td>
<td></td>
<td>(0/1)</td>
<td>(0/1)</td>
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<td>(0/1)</td>
<td>(0/1)</td>
</tr>
<tr>
<td></td>
<td>omero_get_full_images</td>
<td></td>
<td></td>
<td>omero_get_full_images</td>
<td>Get full images from omero</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td>To update</td>
<td></td>
<td>Imaging</td>
<td>omero_get_full_images</td>
<td>lldelisle</td>
<td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
<td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
<td>20240521</td>
<td>fiji</td>
<td>20231211</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
</tr>
<tr>
<td></td>
<td>omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
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3 changes: 2 additions & 1 deletion results/imaging/tools.tsv
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Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu) Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu https://usegalaxy.fr Reviewed To keep
cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.1 (0/1) (0/1) (1/1) (0/1) False
cellpose cellpose Cellpose is an anatomical segmentation algorithm To update https://github.com/MouseLand/cellpose Imaging cellpose bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 3.0.8 cellpose (0/1) (0/1) (1/1) (0/1) False
cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler (0/23) (23/23) (23/23) (19/23) False
cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.6 (0/1) (0/1) (1/1) (1/1) False
bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget (0/1) (0/1) (1/1) (0/1) False
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measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index To update Imaging measure_gastruloids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 20221216 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False
omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down To update Imaging omero_clean_rois_tables lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 20230623 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False
omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id To update Imaging omero_get_children_ids lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0.1.0 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) False
omero_get_full_images omero_get_full_images Get full images from omero To update Imaging omero_get_full_images lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 20240521 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False
omero_hyperstack_to_fluo_measurements_on_gastruloid omero_hyperstack_to_fluo_measurements_on_gastruloid Analyse Hyperstack on OMERO server to measure fluorescence levels To update Imaging omero_hyperstack_to_fluo_measurements_on_gastruloid lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid 20230809 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False
omero_hyperstack_to_gastruloid_measurements omero_hyperstack_to_gastruloid_measurements Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements To update Imaging omero_hyperstack_to_gastruloid_measurements lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements 20240214 fiji 20231211 (0/1) (0/1) (0/1) (0/1) False
upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server To update Imaging upload_roi_and_measures_to_omero lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0.0.5 omero-py 5.11.1 (0/1) (0/1) (0/1) (0/1) False
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