Issues

• API-key access layer for programmatic and agent access

  NL-BioImaging/biomero#93 · Filter by author pmkrawczyk opened on Nov 11, 2026
  

• [BILAYERS] Support multi-select dropdowns

  blockedpriority: P5roadmap
  NL-BioImaging/biomero#91 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Remote Zarr support (e.g. S3)

  blockedpriority: P5roadmap
  NL-BioImaging/biomero#90 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Workflow management: run containers in series

  effort: highimpact: lowpriority: P5roadmap
  NL-BioImaging/biomero#89 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Support schedulers other than Slurm

  effort: highimpact: lowpriority: P5roadmap
  NL-BioImaging/biomero#88 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Improve Slurm jobs with best practices (e.g. schedule outside working hours)

  effort: highimpact: lowpriority: P5roadmap
  NL-BioImaging/biomero#87 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Support other workflow schemas such as CWL

  effort: highimpact: lowpriority: P5roadmap
  NL-BioImaging/biomero#85 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Request less memory for conversion Slurm jobs

  effort: highimpact: lowpriority: P5roadmap
  NL-BioImaging/biomero#84 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Smart auto-batching

  effort: highimpact: mediumpriority: P5roadmap
  NL-BioImaging/biomero#83 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Different job priority for different users

  effort: highimpact: mediumpriority: P5roadmap
  NL-BioImaging/biomero#82 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• SSHFS / fsspec SFTP as an alternative to SCP transfer (for Zarr)

  priority: P5roadmap
  NL-BioImaging/biomero#81 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Integrate with Nextflow

  blockedeffort: mediumimpact: highpriority: P5roadmap
  NL-BioImaging/biomero#80 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• [WF] Deduplicate containers shared by multiple workflows

  priority: P4roadmap
  NL-BioImaging/biomero#79 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• BUG: Slurm accounting reset causes BIOMERO to mix up old data

  impact: highpriority: P4roadmap
  NL-BioImaging/biomero#78 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Support an SSH key per user towards HPC

  effort: highimpact: highpriority: P4roadmap
  NL-BioImaging/biomero#77 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Allow cancelling jobs

  effort: highimpact: mediumpriority: P4roadmap
  NL-BioImaging/biomero#76 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Restrict certain workflows to certain users/groups

  effort: mediumimpact: mediumpriority: P4roadmap
  NL-BioImaging/biomero#75 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• [AI] Could BIOMERO / an AI agent use BioEngine?

  priority: P4roadmap
  NL-BioImaging/biomero#74 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• [BILAYERS] Support remaining Bilayers 1.0.0 functionality

  blockedpriority: P3roadmap
  NL-BioImaging/biomero#73 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Admin-controlled fair-use limits for workflow runs

  priority: P2roadmap
  NL-BioImaging/biomero#72 · Filter by author pmkrawczyk opened on Nov 10, 2026

• Notify users of end-to-end BIOMERO outcomes

  priority: P1roadmap
  NL-BioImaging/biomero#70 · Filter by author pmkrawczyk opened on Nov 10, 2026

• Recover from transient SSH failures without rerunning jobs

  priority: P1roadmap
  NL-BioImaging/biomero#69 · Filter by author pmkrawczyk opened on Nov 10, 2026

• [AI] MCP server for BIOMERO

  priority: P1roadmap
  NL-BioImaging/biomero#68 · Filter by author pmkrawczyk opened on Nov 10, 2026
  

• Reused Slurm job IDs can trigger premature import and destructive cleanup during an active workflow

  NL-BioImaging/biomero#45 · Filter by author RAHoebe opened on Oct 8, 2026
  2

• Reuse OCI layer caches across workflow image builds and reduce Docker-to-SIF installation time

  NL-BioImaging/biomero#44 · Filter by author RAHoebe opened on Sep 29, 2026
  1