OMERO Image Import, Annotation and Region of Interests (ROIs) Workflow Version 1
View on GitHub
Download RO-Crate
Run on GalaxyGeneral workflow to upload data into OMERO using Galaxy
A dataset for testing can be found at: https://zenodo.org/records/14205500
Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Image to Upload in OMERO | Image to Upload in OMERO | Select the image file to upload into OMERO |
|
| Metadata File | Metadata File | Select the metadata file to upload into OMERO. Please refer to the tool "OMERO Metadata Import" to check how the file should be formatted |
|
| OMERO server address | OMERO server address | Please enter a valid OMERO server address to upload your images to. |
|
| ROIs File | ROIs File | Select the ROIs file to upload into OMERO. Please refer to the tool "OMERO ROIs Import" to check how the file should be formatted |
|
| Select Metadata Type | Select Metadata Type | Select if you want metadata as a table (please type "Table") or Key-Value Pairs (please type "Key-Value Pairs") |
|
| Target Dataset | Target Dataset | Select a target dataset to upload the image to. If the dataset name does not exist in OMERO, a new dataset will be created automatically. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | OMERO Image Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_import/omero_import/5.18.0+galaxy3 |
| 7 | Convert | Convert characters1 |
| 8 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
| 9 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 |
| 10 | Parse parameter value | param_value_from_file |
| 11 | OMERO Metadata Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_metadata_import/omero_metadata_import/5.18.0+galaxy3 |
| 12 | OMERO ROI Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_roi_import/omero_roi_import/5.18.0+galaxy4 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| image_upload_log | image_upload_log | n/a |
|
| metadata_import_log | metadata_import_log | n/a |
|
| log | log | n/a |
|
Version History
Version 1 (earliest) Created 28th Jan 2025 at 13:17 by Riccardo Massei
Initial commit
Open
master802e6ac
Creators and Submitter
Views: 48 Downloads: 7 Runs: 0
Created: 28th Jan 2025 at 13:17
AttributionsNone
Related items
https://orcid.org/0000-0003-2104-9519
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, MOLGENIS, 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, 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, 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, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, OLCF-WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions, RenLabBioinformatics, Yongxin's team, PiFlow, HLee_SeoGroup, UFZ - Image Data Management and Processing Workflows, Korean Bioinformaticians, Into the deep, XChem, CPM, SocialGene, Research Data Management ICE-2, ObjectRecognition, LiDAR, FONDA II C2, Senckenberg Digital Collection and Biodiversity Information Technologies, Astroparticle Lab
Web page: Not specified
Space: Independent Teams
Public web page: Not specified
