0.4.0

Overview

In this release we move recOrder's reconstructions to a configuration-file-based command-line interface. All reconstructions from the GUI make CLI calls that are exactly reproducible.

Key changes

• configuration-file-based CLI
• torch computations for all reconstructions, enabled by waveorder
• on-the-fly birefringence overlays
• napari sample contributions

What's Changed

• Pin README links by @talonchandler in #345
• Test docking the plugin widget by @ziw-liu in #346
• Run CI/CD tests on all PRs by @talonchandler in #383
• 0.4.0dev merge to main by @talonchandler in #375
• Bump dependencies and enable widget test by @ziw-liu in #391
• 0.4.0 installation documentation by @talonchandler in #395
• Reconstruct a subset of time indices by @talonchandler in #398
• Pass scale metadata through recorder reconstruct by @talonchandler in #399
• Remove recorder view by @talonchandler in #400
• Skip QFileDialog.Options() by @talonchandler in #404
• Standardize CLI by @talonchandler in #402
• "Flip Orientation" and "Invert Phase Contrast" GUI checkboxes by @talonchandler in #405
• CLI creates empty HCS zarr then fills it by @talonchandler in #408
• Bump to iohub==0.1.0.dev5 by @talonchandler in #414
• GUI save to plate by @talonchandler in #415
• Refactor apply_inverse_transfer_function file for multiprocessing by @talonchandler @edyoshikun in #411
• Check for PyQt5 by @talonchandler in #420
• Simplify Dask graph before computing overlay by @ziw-liu in #423
• Clean deprecated by @talonchandler in #422
• Retardance reconstructions in nm by @talonchandler in #413
• recOrder data schema by @talonchandler in #421
• Implement schema by @talonchandler in #424
• Redo overlay2 by @talonchandler in #425
• Improved birefringence overlays by @talonchandler in #426
• 0.4.0 revised documentation by @talonchandler in #428
• "Orientation Legend" -> "Visualization" tab by @talonchandler in #431
• Background scaling, naming, and squeezing by @talonchandler in #429
• Sample contribution merge to main by @talonchandler in #434
• Squeeze scale with image by @talonchandler in #435
• 0.4.0 release fixes by @talonchandler in #436

Full Changelog: 0.3.0...0.4.0