Image analysis using CellProfiler (EOSC-Life D6) Version 2
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Run on usegalaxy.euThis workflow has been created as part of Demonstrator 6 of EOSC-Life WP3 and is focused on reusing publicly available RNAi screens to gain insights into the nucleolus biology. The workflow downloads images from the Image Data Resource (IDR), performs object segmentation (of nuclei and nucleoli) and feature extraction of the images and objects identified.
Steps
| ID | Name | Description |
|---|---|---|
| 0 | Starting modules | Detail the metadata associated to the images that will be processed toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9 |
| 1 | Download images | toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41 |
| 2 | Segment complete nuclei | Incomplete nuclei that are touching the borders of the image are ignored and therefore, not segmented. It doesn't include the nuclei outside the diameter range either. toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 |
| 3 | Segmentation mask complete nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 |
| 4 | Label nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9 |
| 5 | Save labelled nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9 |
| 6 | Detect dark holes in nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9 |
| 7 | Segment nucleoli that fall inside nuclei | The dark holes enhanced in the previous step are segmented only if they are inside a nuclei toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9 |
| 8 | Segment nucleoli | The segmentation only affects those inside the nuclei toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 |
| 9 | Convert the segmented nucleoli into an image | toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 |
| 10 | Combine masks (nuclei + nucleoli) | toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9 |
| 11 | Save combined segmentation masks | toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9 |
| 12 | Segment all nuclei | Incomplete nuclei that are touching the borders of the image are segmented, also the nuclei outside the diameter range. toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 |
| 13 | Segmentation mask nucleoli including cells touching borders | toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 |
| 14 | Extract background | toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0 |
| 15 | Measure the image granularity | This step measures the granularity of the original image toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9 |
| 16 | Measure the nuclei texture | This step measures the texture of the original image and nuclei in it toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9 |
| 17 | Measure the nuclei intensity | This step measures the intensity of the original image and the nuclei toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9 |
| 18 | Measure size and shape of nuclei and nucleoli | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9 |
| 19 | Relate nucleoli with their parent nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9 |
| 20 | Measure the image quality | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9 |
| 21 | Measure the area occupied by nuclei and nucleoli | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9 |
| 22 | Measure the image intensity | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9 |
| 23 | Export measurements | toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9 |
| 24 | Run CellProfiler | toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9 |
Outputs
| ID | Name | Description | Type |
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| _anonymous_output_1 | _anonymous_output_1 | n/a |
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| _anonymous_output_2 | _anonymous_output_2 | n/a |
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| _anonymous_output_3 | _anonymous_output_3 | n/a |
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| _anonymous_output_4 | _anonymous_output_4 | n/a |
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| _anonymous_output_5 | _anonymous_output_5 | n/a |
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| _anonymous_output_6 | _anonymous_output_6 | n/a |
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| _anonymous_output_7 | _anonymous_output_7 | n/a |
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| _anonymous_output_8 | _anonymous_output_8 | n/a |
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| _anonymous_output_9 | _anonymous_output_9 | n/a |
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| _anonymous_output_10 | _anonymous_output_10 | n/a |
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| _anonymous_output_11 | _anonymous_output_11 | n/a |
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| _anonymous_output_12 | _anonymous_output_12 | n/a |
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| _anonymous_output_13 | _anonymous_output_13 | n/a |
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| _anonymous_output_14 | _anonymous_output_14 | n/a |
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| _anonymous_output_15 | _anonymous_output_15 | n/a |
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| _anonymous_output_16 | _anonymous_output_16 | n/a |
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| _anonymous_output_17 | _anonymous_output_17 | n/a |
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| _anonymous_output_18 | _anonymous_output_18 | n/a |
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| _anonymous_output_19 | _anonymous_output_19 | n/a |
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| _anonymous_output_20 | _anonymous_output_20 | n/a |
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| _anonymous_output_21 | _anonymous_output_21 | n/a |
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| _anonymous_output_22 | _anonymous_output_22 | n/a |
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| _anonymous_output_23 | _anonymous_output_23 | n/a |
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| _anonymous_output_24 | _anonymous_output_24 | n/a |
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| _anonymous_output_25 | _anonymous_output_25 | n/a |
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| _anonymous_output_26 | _anonymous_output_26 | n/a |
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Version History
Version 2 (latest) Created 3rd Nov 2020 at 22:12 by Beatriz Serrano-Solano
Open
master34f1bfc
Creators and SubmitterViews: 3012 Downloads: 58
Created: 24th Jun 2020 at 22:00
Last updated: 3rd Nov 2020 at 22:12
AttributionsNone
Related items
Teams: IBISBA Workflows, EOSC-Life WP3
Organizations: Unspecified, EMBL-EBI
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, Genomics Coordination Center, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Galaxycompchem, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Cluster Emergent del Cervell Humà, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, DARE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, DLSW, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES
Web page: Not specified
Workflows from the Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project, which is funded by the European Union Horizon 2020 program INRAIA-02 under grant agreement 730976.
The workflows also appear on https://hub.ibisba.eu
Space: Independent Teams
Public web page: https://www.ibisba.eu
