Biomero

Latest version: v1.14.0

Safety actively analyzes 710445 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 1 of 12

2.0.0alpha.3

- Also read config from /OMERO/slurm-config.ini (after /etc but before ~ ). This location is shared between OMERO containers generally.

**Full Changelog**: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha.2...v2.0.0-alpha.3

2.0.0alpha.2

- Expand ~ to read config from user home dir.

**Full Changelog**: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha.1...v2.0.0-alpha.2

2.0.0alpha.1

- Add the `SlurmClient.from_config(config_only=True)` option to load a lighter version of the SlurmClient that doesn't actually connect with Slurm or the database. This can be used for information / config calls, like finding out what workflows are configured.

**Full Changelog**: https://github.com/NL-BioImaging/biomero/compare/v2.0.0-alpha...v2.0.0-alpha.1

2.0.0alpha

- Add full BIOMERO workflow execution tracking through eventsourcing and a postgres database

**Full Changelog**: https://github.com/NL-BioImaging/biomero/compare/v1.14.0...v2.0.0-alpha

1.14.0

- Bump to 1.14.0 for BIOMERO scripts update for duplicate parameter names
- Setup for multiple measurements workflows

**Full Changelog**: https://github.com/NL-BioImaging/biomero/compare/v1.13.0...v1.14.0

1.13.0

- Allow pulling a conversion container instead of building it on Slurm. This reduces the rights required on Slurm for BIOMERO.
- We build and release our default converter with every BIOMERO version `cellularimagingcf/convert_zarr_to_tiff`, even if there are no changes. Just to be sure there is always a 'compatible' version to go with your BIOMERO version, which is true for the old way of doing it.
- This image can be added in the `slurm-config.ini` under a new `[CONVERTERS]` subsection.
- When you init the Slurm environment, it will check for this config and download this converter image. If there is no such config, it will default to previous behavior (which is building a Singularity image on the Slurm server itself).
- Example setting:

[CONVERTERS]
-------------------------------------
Converters settings
-------------------------------------
Settings for linking to external converters.

By default, BIOMERO exports images as ZARR to the HPC.
But, the workflow you want to execute might require
a different filetype. E.g. most of our example workflows
require TIFF input files.

By default we will build a converter on Slurm for you.
Theoretically you can add other converters here to pull
those instead. These should be available on dockerhub.

-------------------------------------
ZARR TO TIFF
-------------------------------------
Uncomment this if you want to pull the image instead of
build it. E.g. if you don't have singularity build rights
on your Slurm.

Please pin it to a specific version to reduce unforeseen errors.

Key should be the types "X_to_Y" and value should be the docker image
zarr_to_tiff=cellularimagingcf/convert_zarr_to_tiff:1.13.0



**Full Changelog**: https://github.com/NL-BioImaging/biomero/compare/v1.12.0...v1.13.0

Page 1 of 12

© 2025 Safety CLI Cybersecurity Inc. All Rights Reserved.