0.4.2rc1

0.4.2 release candidate.

What's Changed

• Append channels via CLI calls by @talonchandler in #454
• Bump python versions by @ziw-liu in #455
• Optional GUI/PM dependencies by @ziw-liu in #456
• Chunk transfer functions by @talonchandler in #463
• Pass metadata by @talonchandler in #464
• Collect and unify color overlays by @talonchandler in #473
• Pin ome-zarr by @talonchandler in #475
• Fix background-check bug by @talonchandler in #469
• Default HSV colormap by @talonchandler in #471
• Bump Python, iohub, and waveorder by @ziw-liu in #478

Full Changelog: 0.4.1...v0.4.2rc1

0.4.1

• improved README and sample contributions

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

0.3.1

Patch release with improved installation documentation.

0.4.0rc0

• pre-release for testing the usbdrvd.dll driver
• when 0.4.0 is ready, create a new release, update the links to the USB driver in docs/microscope-installation-guide.md, push to PyPI, then delete this 0.4.0rc0 release from github

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

0.2.1

This a maintenance release to resolve upstream dependency issues. The functionalities are the same as v0.2.0.

Full Changelog: 0.2.0...0.2.1

0.2.0

Overview

In this release, we improved core functionality (calibration and background corrections), usability, and fixed several bugs. This release is almost entirely backwards compatible, and the user will be alerted when backwards compatibility has been broken to fix a bug.

Key changes:

• Improved stability of liquid crystal calibration with low swing values
• Reliable background correction options with clearer names
• Updated Micro-Manager dependency to nightly build 2022-09-20
• Removed features not specific to label-free microscopy -- fluorescence, registration, and denoising
• Improved documentation
• User interface bug-fixes and usability features
• Python version bumped to 3.8+
• This software is now licensed under BSD 3-Clause license
• Initial support for calibrating the LC in "voltage mode" and "DAC mode", in preparation of hardware-sequencing of polarization states (stay tuned!)

What's Changed

• Update calibration_data_class branch by @ieivanov in #96
• Calibration data class by @ieivanov in #105
• Improved testing, configs, and dev tools by @talonchandler in #112
• Metadata update by @ieivanov in #117
• Fix warnings when all layers are deleted: issue #113 by @talonchandler in #118
• Pin pycromanager and MicroManager versions by @talonchandler in #119
• Add ome-tiff reader to recOrder (via waveorder) by @talonchandler in #122
• Calibration data class v2 by @ieivanov in #116
• Fix ome-tif to zarr converter for acquisitions with micromanager beta by @talonchandler in #123
• Updates to LC calibration by @ieivanov in #127
• Update license by @mattersoflight in #145
• Correct 'global' and 'local_fit' background corrections by @talonchandler in #139
• Restructure tests by @ieivanov in #140
• Test calibration imports by @talonchandler in #151
• Move docs from wiki to /docs/ by @talonchandler in #132
• Convert GUI-acquired data to zarr before reconstruction by @talonchandler in #146
• Improve help messages for recOrder's CLI by @talonchandler in #133
• Pycromanager converter v2 by @ieivanov in #148
• Don't delete test data? by @talonchandler in #159
• BSD 3-clause by @talonchandler in #161
• CLI regression fix and end-to-end CLI test by @talonchandler in #158
• Require importlib-metadata by @talonchandler in #150
• Check for equal exposures across channels by @talonchandler in #162
• Fix background correction for non-square images and online mode by @talonchandler in #167
• Don't update calibration metadata by @talonchandler in #163
• Update shutter behavior and LF acquisition channel order by @ieivanov in #160
• Print RAM warning message in online and offline modes by @talonchandler in #157
• Remove background averaging by @talonchandler in #169
• Clean dependencies by @talonchandler in #171
• Show RAM warning in GUI / log in CLI by @ziw-liu in #174
• Set focus to "Plot" tab by default by @talonchandler in #173
• Improved warning message by @talonchandler in #175
• Hide "listen" and "overlay" features from recOrder GUI by @talonchandler in #177
• Always load background and warn if background and image sizes are mismatched by @talonchandler in #181
• Capture Background without calibration yields a warning by @talonchandler in #178
• Mismatched x/y size of background and acquisition should error instead of warn by @talonchandler in #182
• Initialize calibration values when loading from metadata files by @ziw-liu in #184
• Upgrade pycromanager and micromanager by @talonchandler in #183
• Development guide by @talonchandler in #185
• OSX_arm64 dev install and Markdown linting by @ziw-liu in #165
• Refactor calibration workers and fix metadata writing by @ziw-liu in #195
• Mapping capture background path from calibration to reconstruction by @edyoshikun in #196
• GUI development docs by @talonchandler in #201
• Hide "Use Cropped ROI" checkbox by @talonchandler in #206
• Remove pre-acquisition background file check for 'Estimated' background correction by @ziw-liu in #202
• Remove "pad_z" from the expected microscope metadata by @ziw-liu in #208
• Plot calibrated LC states by @ziw-liu in #199
• Save background reconstruction and visualization by @ziw-liu in #209
• Fix bug in calibration_metadata writer by @ieivanov in #212
• Remove fluorescence, preprocessing, and postprocessing; simplify GUI by @talonchandler in #210
• Fix 'Capture Background' when MM is in 'Live' mode by @ziw-liu in #205
• fixing the issue to connect and reconnect to MM by @edyoshikun in #198
• Recommend MM 2022-09-20 by @talonchandler in #215
• Fix silent calibration failures by @talonchandler in #214
• Fix 'Load Default Config' in offline mode by @ziw-liu in #226
• Reduce "Value" in default overlay by @talonchandler in #223
• Remove microscope parameters from calibration metadata by @ziw-liu in #227
• 0.2.0 integration PR by @talonchandler in #219
• Block imageio versions that cause import error by @ziw-liu in #228

Full Changelog: 0.1.2...0.2.0

New Contributors

• @ziw-liu made their first contribution in #174
• @edyoshikun made their first contribution in #196

0.1.2

This patch updates the license to BSD 3-clause.

0.1.1

This patch pins waveorder to version 1.0.0b0 so that future waveorder releases do not break production.