0.3.0

Overview

In this release we focus on enhancing recOrder's interactive snap-and-reconstruct workflow. The functionality exposed in the GUI is more robust and reproducible.

Key changes

• The unstable offline reconstruction CLI has been temporarily removed in preparation for an overhaul in the next release
• Added example scripts to help users transition to the new offline reconstruction workflow
• Updated the image file format generated by the GUI upgraded from OME-NGFF v0.1 to v0.4 (latest)
• Changed file I/O dependency from waveorder to iohub
• Parameters set in the GUI are now saved in gui_state.yml with acquired data for better reproducibility
• Improved algorithm for extinction evaluation
• Polarization channels are averaged over Z in 2D mode for better SNR if a Z-stack is acquired for phase reconstruction
• Simplified acquisition GUI
• Supported Python versions bumped to 3.9-3.11

What's Changed

• Introduce Black formatting into the code base by @ziw-liu in #229
• git blame ignore squashed commit hash by @talonchandler in #232
• Test MM Core calls with mocks by @ziw-liu in #239
• Remove offline mode by @talonchandler in #241
• Turn off autoshutter before bg capture by @ieivanov in #245
• Simplify acquisition settings by @talonchandler in #246
• Bump napari-hub-preview-action version to fix CI by @ziw-liu in #251
• Update development guide to install waveorder for co-development by @ziw-liu in #233
• 90 degree orientation offset checkbox by @talonchandler in #248
• Import qtpy instead of PyQt5 in autogenerated gui.py by @talonchandler in #252
• Reconstruction scripts w/ documentation by @talonchandler in #249
• Override initial tab to focus on 'LC Calibration' by @ziw-liu in #256
• Rename acquisition buttons and move "Phase from BF" checkbox to its own button by @talonchandler in #260
• Remove background debugging print statement by @talonchandler in #261
• Rename "90 Degree Offset" to "Orientation Offset (90 deg) by @talonchandler in #267
• Move the most recent layer to the top of the layers list by @ziw-liu in #264
• Use HSV colormap for the background orientation layer by @ziw-liu in #269
• Draw overlay for both 2D and 3D birefringence acquisitions by @ziw-liu in #270
• "Retardance + Orientation + Phase" in 2D mode averages over z for retardance and orientation instead of slicing by @talonchandler in #274
• Read illumination parameters from the loaded calibration instead of GUI during acquisition by @ziw-liu in #273
• Add ROI size check for the previous phase reconstructor by @ziw-liu in #275
• Add 3D->2D phase script and add in_focus_slice argument by @talonchandler in #284
• Check for non-physical NA arguments by @talonchandler in #288
• Populate "BF Channel" list with presets containing keywords by @talonchandler in #287
• Dependency cleanup by @ziw-liu in #283
• Save GUI state with snapped images by @ziw-liu in #279
• Set NA defaults by @talonchandler in #291
• Improve example scripts by @talonchandler in #289
• Keep shutter open during 2D phase acquisitions by @talonchandler in #292
• Restore previous MDA settings after acquisition by @ziw-liu in #286
• fix BF channel index in 3D-pol-to-birefringence example by @ieivanov in #295
• Disable "Phase From BF" button when no BF channel is found - add tooltip by @talonchandler in #294
• Pin NumPy version by @ziw-liu in #301
• Fix tests by @talonchandler in #302
• recorder info and recorder view command-line utilities by @talonchandler in #297
• Swing-invariant extinction ratio and documentation by @talonchandler in #308
• Link to calibration guide from index by @talonchandler in #310
• Example script saves to a single zarr by @talonchandler in #298
• Update setup.cfg for macos_arm64 specific dependencies by @mattersoflight in #313
• Move imports into cli functions by @talonchandler in #317
• Updated Pycromanager to 0.24.1. by @nicost in #307
• Transpose + np.copy() + (fancy indexing and/or ndarray.copy()) causes major slowdowns by @talonchandler in #322
• Depend on iohub by @talonchandler in #331
• Multiprocessing script for reconstructing multiple positions and times by @talonchandler in #332
• Depend on iohub tagged release by @talonchandler in #333
• Add overlay option to view command by @talonchandler in #336
• Turn live mode off when loading calibration by @talonchandler in #335
• Write to single zarr store by @talonchandler in #340
• Install iohub from PyPI by @ziw-liu in #342
• Minor documentation updates for 0.3.0 by @talonchandler in #344

New Contributors

• @nicost made their first contribution in #307

Full Changelog: 0.2.1...0.3.0