v0.5.1

What's Changed

Minor fix for Docker deployment and documentation

Full Changelog: v0.5.0...v0.5.1

v0.5.0

What's Changed

Rework of Backsub to not have Palom as a dependency reducing the environment size and making it lightweight, and reducing the output file size, while keeping the time and memory usage efficiency.

Added

• compression parameter
• two RAM profiles: (1) default, uses moderate RAM. (2) Uses approximately half of the default RAM at the cost of a slight loss in precision of the calculation of the downsized dimensions of the pyramidal output image. This means the dimensions of the pyramidal level will differ between profile 1 and 2. The high-resolution level is not affected by this.
• organizes the tool in five scripts: (1) CLI, (2) ome-schema structure, (3) ome-schema writer, (4) background subtraction and writing of output image and (5) extraction of metadata from Lunaphore COMET images to create the marker table.
• restructured README
• tile-size parameter now defaults to 256 instead of 1024
• support for different data types - primarily np.uint8 in addition to np.uint16
• Added validation and warnings for invalid or missing backgrounds
• Necessary prerequisites for PyPI release

Fixed

• output image file-size is reduced by applying lossless compression ("LZW" by default)
• Updated documentation, Dockerfile, and environment setup
• Improved logging system and CLI descriptions

Removed

• Palom and OpenCV as dependencies
• old scripts, version history should be checked instead.
• chunksize argument - chunking is done now only by the default dask.array behaviour

Full Changelog: v0.4.1...v0.5.0

v0.4.1

• Reworked Backsub to increase RAM-efficiency
• implemented Palom's pyramid writer
• added delayed calculation execution
• added --chunk-size parameter

v0.4.1-test2

Testing to see if new version build correctly.

v0.3.4

Added '--pyramid' (True or False, default True)
Added '--version' (prints version and exits)
Added '--tile-size' (default 1024)

v0.3.3

Fixed overflow issue

v0.3.2

Added procps-ng to the list of dependencies for the Docker image.
Supports Nextflow commands such as -with-report and similar now.

v0.3.1

Added any channel subtraction specified with the "background" column in the markers.csv
Uncoupled channel removal from background channel definition with the "remove" column in the markers.csv

v0.3.0

Added any channel subtraction specified with the "background" column in the markers.csv
Uncoupled channel removal from background channel definition with the "remove" column in the markers.csv

v0.2.0

Added Python to PATH and specified WORKDIR
Fix for Singularity