v1.14.0

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

Full Changelog: v1.13.0...v1.14.0

v1.13.0

• 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: v1.12.0...v1.13.0

v1.13.0-alpha.6

Full Changelog: v1.13.0-alpha.5...v1.13.0-alpha.6

v1.13.0-alpha.5

Full Changelog: v1.13.0-alpha.4...v1.13.0-alpha.5

v1.13.0-alpha.4

Full Changelog: v1.13.0-alpha.3...v1.13.0-alpha.4

v1.13.0-alpha.3

Full Changelog: v1.13.0-alpha.2...v1.13.0-alpha.3

v1.13.0-alpha.2

Full Changelog: v1.13.0-alpha.1...v1.13.0-alpha.2

v1.13.0-alpha.1

Full Changelog: v1.13.0-alpha...v1.13.0-alpha.1

v1.13.0-alpha

• Builds the converter image so that we can pull it instead of build it

Full Changelog: v1.12.0...v1.13.0-alpha

v1.12.0

• Conversion ZARR to TIFF: write TIFF with extra metadata for (handling of > 3 channels in) cellprofiler/imagej

Full Changelog: v1.11.0...v1.12.0