Welcome to BIOMERO’s documentation!

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BIOMERO - Get Started

• BIOMERO - BioImage analysis in OMERO
• Overview
• Quickstart
• Prerequisites & Getting Started with BIOMERO
  • Slurm Requirements
  • OMERO Requirements
  • Getting Started
• BIOMERO scripts
• (Docker) containers
• See the tutorials
• SSH
• SlurmClient class
• slurm-config.ini
  • Time Limit on Slurm
• How to add an existing workflow
  • Workflow metadata via descriptor.json
    • Schema
  • Multiple versions
  • I/O
    • Wrapper.py
• How to add your new custom workflow
• Slurm jobs
  • Generating jobs
  • How to add your own Slurm job
    • Parameters
• Batching
• Using the GPU on Slurm
• Transfering data
• Testing the Python code
• Logging

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Tutorials

• Cellprofiler tutorial
  • 0. Prerequisite: OMERO, Slurm and biomero.
  • 1. Grab the data and pipeline
  • 2. Try the pipeline locally
  • 3. Upload the data to OMERO
  • 4. Package the cellprofiler in a FAIR package
  • 5. Add this workflow to the OMERO Slurm Client
  • 6. Add a OMERO script to run this from the Web UI
  • Extra: How to add workflow parameters to cellprofiler?
  • Extra 2: We should add a LICENSE
• CellExpansion tutorial
  • Introduction
  • 1. Import data to OMERO
  • 2. Extract masks with Cellpose
  • 3. CellExpansion
  • Calculate overlap
  • Workflow management?
  • Extra
• Local Slurm tutorial
  • Introduction
  • 0. Requirements
  • 1. Setup Docker containers for Slurm
  • 2. Add SSH access
  • 3. Test Slurm
  • 4. OMERO & OMERO Slurm Client
  • 5. Workflows!
• Google Cloud Slurm tutorial
  • Introduction
  • 0. Requirements
  • 1. Setup Google Cloud for Slurm
  • 2. Add SSH access
  • 3. Test Slurm
  • 3b. Install requirements: Singularity / Apptainer and 7zip
  • 4. OMERO & OMERO Slurm Client
  • 5. Workflows!
• Microsoft Azure Slurm tutorial
  • Introduction
  • 0. Requirements
  • 1. Setup Microsoft Azure for Slurm
  • 1 - Addendum - Setting up Slurm Accounting DB
  • 2. Test Slurm
  • 3. Test Singularity on Slurm
  • 5. Setting up (BI)OMERO in Azure too (Optional)
  • 6. Showtime!
• Extra thoughts

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Package

• biomero
  • biomero package
    • biomero.slurm_client module

Indices and tables

• Index