BIOMERO

BIOMERO - Get Started

  • BIOMERO BIOMERO — BioImage Analysis in OMERO
  • BIOMERO BIOMERO 2.0
  • BIOMERO Python library (BIOMERO.analyzer)
  • Quickstart
  • Prerequisites & Getting Started with BIOMERO
  • BIOMERO.scripts
  • BIOMERO Web Interface
  • (Docker) containers
  • See the tutorials
  • Developer: Eventsourcing and Views
  • SSH
  • SlurmClient class
  • slurm-config.ini
  • How to add an existing workflow
  • How to add your new custom workflow
  • Slurm jobs
  • Batching
  • Using the GPU on Slurm
  • Transfering data
  • Testing the Python code
  • Logging
  • BIOMERO components
  • Citing BIOMERO

Tutorials

  • Cellprofiler tutorial
  • CellExpansion tutorial
  • Local Slurm tutorial
  • Google Cloud Slurm tutorial
  • Microsoft Azure Slurm tutorial
  • Extra thoughts
  • OMERO workflow scripts

Configuration

  • SLURM Configuration Guide
  • Configuration Reference

Package

  • biomero

Developer

  • Eventsourcing and Views (Developer)
  • Execution, storage and recovery
  • Workflow metadata views
BIOMERO
  • Overview: module code
  • NL-BioImaging/biomero

All modules for which code is available

  • biomero.eventsourcing
  • biomero.maintenance
  • biomero.provenance
  • biomero.remote_shallower
  • biomero.slurm_client
  • biomero.views

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