NGFF-Converter 2.0

[DavidStirling]

Fixes #54, closes #45, closes #44, closes #43, fixes #39, resolves #38, fixes #34, resolves #26.

This PR contains NGFF-Converter 2.0, which is practically a total rebuild of the tool intended to modularise the conversion process, improve the GUI and make the whole experience smoother for users.

Previously OME-TIFF mode was basically a hack, and the utility was charged with generating arguments for the bioformats2raw/raw2ometiff CLIs. In this version we can define a proper, modular sequence of steps which directly interface with the tool APIs. This will make NGFF-Converter more extensible in the future.

Per the changelog:

Features:

• Redesigned user interface, modernised layout and design.
• NGFF-Converter now directly interfaces with bioformats2raw/raw2ometiff instead of generating a CLI call.
• Modularised conversion into "Jobs" (internally called "Workflows") comprised of a sequence of "Tasks".
• Added virtual "Output" task to control destination files.
• Added full settings configuration panels for all tasks.
• Added progress bars per-task during execution.
• Revised configuration workflow. Settings are now initialised to user-defined defaults. Jobs can be configured individually or in bulk.
• Job execution now uses a proper queue, so jobs can be started/stopped individually.
• Execution logs are now stored and delivered per-job.
• Added configuration options for working directory and log directory (if logging to file).

Bugfixes/Maintenance:

• Updated component package versions
  • bioformats 7.1.0
  • bioformats2raw 0.9.1
  • raw2ometiff 0.7.0
• Updated documentation

Known issues:

• The underlying bioformats package is currently unable to read some formats on ARM-based MacOS systems.
• raw2ometiff execution cannot be reliably interrupted until it finishes the initial scan of a .zarr file.

[will-moore]

This looks great. Keen to give it a try, but I see that it's not available at https://downloads.glencoesoftware.com/public/NGFF-Converter/latest/ yet?

I wondered if it would be worth adding that link to the README of this repo, since there's no obvious way to download the app if you're starting here?
Cheers!

[DavidStirling]

We're currently working on code signing the release assets, so hope to have the release launched in the next day or so.

Cross-linking the readme is a great idea though, will do that.