Lumos v0.1.1

Description

Lumos v0.1.1 release by @tlp19 in #4 and #6.

The new version of Lumos contains small fixes as well as a new README.

Changelog

• Fix issue when using the parallelism argument where no images would be generated.
• Fix issue with the --single-well argument where wells with names containing lowercase characters could not be matched.
• New README.

Lumos v0.1

Description

Lumos v0.1 release by @tlp19 in #3

This new version of Lumos aims at making the program more configurable and usable by other sources of the JUMP-CP consortium.

Lumos v0.1 - Changelog

Refactorings

• Extracted build_input_images_df() as a toolbox function.
• Extracted concatenate_images_in_grid() as a toolbox function.
• Removed duplicates of configuration parameters.
• Moved configuration parameters to a YAML file.

Improvements

• Made Lumos compatible with different file-naming schemes and folder structures.
• Made Lumos compatible with other plate formats (custom well and site grid-patterns).
• Allow a custom YAML configuration file to be specified when launching Lumos.
• Add a command to generate a template of a configuration file.
• Add option to disable logs (--disable-logs), useful for running tests with pytest.

Testing

• Added new pipeline tests for both QC and CP modes that use custom configuration files.
• Added a new unit test for toolbox.concatenate_images_in_grid().

GitHub Workflows

• Added a pylint linting workflow on every push that modifies the codebase.
• Added a pytest testing workflow on every pull request that modifies the codebase.

Known issues

In this version, the --parallelism argument is broken and no images are generated. This is fixed in the next version v0.1.1.

Lumos v0.0.4

Description

Lumos v0.0.4 release by @tlp19 in #2

This version provides some new simple functionalities to the program as well as some fixes.

Changelog

New functionalities:

• New 'sites' scope for Cell Painting mode (outputs one cell-painted image per site)
• Ability to generate cell-painted images for only one well (for both 'wells' and 'sites' scopes)
• Option to choose the output image file format (either JPEG or PNG)
• Added functionality to display the compound identifier of each well, which is parsed from the platemap of the plate (columns to be parsed can be configured)

Improvements:

• Code refactorings in picasso.py
• Improved high-level tests that now rely on the CLI
• Calibration of cell-painting image-tuning parameters on DMSO-only plate
• Improved documentation for developers in readme-dev.md

Fixes:

• Fix intensity overflow when multiplying 8-bit images by channel coefficients (in both QC and CP)
• Fix typos in codebase and readmes

Miscellaneous:

• Code linting
• Updated HTML documentation
• Improved CLI help menus and dialogs (with color-coding)

Lumos v0.0.3

Description

Lumos v0.0.3 release by @tlp19 in #1

New version of Lumos that includes a new Cell-Painting mode and various Quality Control feature enhancements.

Changelog

See the full detailed changelog in the Pull Request description of #1

Lumos V0.0.2

First release of lumos used on the Yokogawa PC

First development focused mainly on windows 10 use.