3.0.5

What's Changed

• Tile Stitch Engine by @srivarra in #559
• Shift-variant fluorescence simulation, Zernike recovery, and bench cases by @talonchandler in #560
• feat(zernike,phantoms): SeidelPupil + ring-bead phantoms by @talonchandler in #561
• fix(bench): update ops path to /hpc/projects/icd.fast.ops by @talonchandler in #565

Full Changelog: 3.0.4...3.0.5

3.0.4

What's Changed

• Use ProcessPoolExecutor with spawn for apply-inv-tf workers by @ieivanov in #558

Full Changelog: 3.0.3...3.0.4

3.0.3

What's Changed

• Add benchmarking suite by @talonchandler in #551
• Warn on pixel size mismatch and add --write-config-scale-to-output flag by @talonchandler in #546
• Namespace reconstruction settings by output channel names by @talonchandler in #547
• Replace create_empty_hcs_zarr with iohub's create_empty_plate by @ieivanov in #554
• Defer chunk/shard choice to iohub by @ieivanov in #555
• Update AQLM demo notebooks by @talonchandler in #556
• Reference checks for benchmark regression tracking by @talonchandler in #553
• Update iohub to 0.3.4 by @ieivanov in #557

Full Changelog: 3.0.2...3.0.3

3.0.2

What's Changed

• Support OME-Zarr v0.5 (Zarr v3) datasets by @talonchandler in #519
• Batched focused slice by @edyoshikun in #522
• Refactor: add xarray API layer and clean up CLI layer by @talonchandler in #520
• Parameter optimization for phase and fluorescence reconstructions by @talonchandler in #525
• Reconstruction optimization and GPU support by @talonchandler in #532
• iohub dependency by @ieivanov in #543
• Loosen iohub dependency to >=0.3.0a6,<0.4 by @talonchandler in #536
• Optimization infrastructure: pluggable backends, losses, batched GPU processing by @talonchandler in #531
• Fix dynamic versioning pattern to match unversioned tags by @talonchandler in #548

New Contributors

• @edyoshikun made their first contribution in #522

Full Changelog: 3.0.0...3.0.2

3.0.1

-hotfix commit 47f8a54 added on top of 3.0.0

Bug fixes

• Fix AttributeError: 'torch.dtype' object has no attribute 'name' when reconstructing into OME-Zarr v0.5 (zarr v3) stores (#519)
• Fix KeyError on v0.5 plate metadata extraction (#519)
• Output zarr version now matches input zarr version (#519)

Dependency changes

• Bumped iohub minimum from >=0.2 to >=0.3.0a3 to ensure zarr v3 support

3.0.0

What's Changed

• Fix installation by @talonchandler in #184
• Fix style by @talonchandler in #185
• Fix pytests by @talonchandler in #186
• Clean up examples and temp files by @talonchandler in #187
• Remove recorder image references by @talonchandler in #189
• Merging README by @mattersoflight in #188
• Merge recOrder into waveorder by @talonchandler in #183
• Bump iohub and pydantic by @ziw-liu in #448
• Test on click 8.2.0 by @ziw-liu in #450
• Fix 3D to 2D phase reconstruction by @talonchandler in #441
• Settings-ratio checks should give warnings, not errors by @talonchandler in #452
• bug in monitor by @ahillsley in #445
• Remove submitit dependency by @talonchandler in #454
• Skip reconstructions of empty FOVs by @ieivanov in #457
• Instructions to install from pip and github by @talonchandler in #451
• Gui update by @amitabhverma in #458
• Documentation infrastructure by @amitabhverma in #461
• Vector prototype CLI by @talonchandler in #440
• Refactor compute_midband_power by @talonchandler in #471
• run tests on pr by @tlambert03 in #477
• simplify test ci by @tlambert03 in #478
• tests: run example tests on ci and mock show by @tlambert03 in #476
• Exclude docs/, tests/, etc. from wheel by @talonchandler in #480
• Faster tests by @talonchandler in #487
• Handle single position .zarr stores as CLI input by @talonchandler in #486
• Fixes loading default phase.yml and fluorescence.yml config files in GUI by @amitabhverma in #488
• Improve installation instructions by @talonchandler in #479
• Package layout fix by @talonchandler in #489
• Visual assets appear in plugin by @talonchandler in #495
• Bump iohub by @talonchandler in #492
• 2D fluorescence reconstruction by @talonchandler in #460
• demos for AQLM 2025 by @mattersoflight in #446
• Updated to Pydantic V2 Models by @srivarra in #508
• Update is_single_position_store to catch FileNotFoundError by @talonchandler in #509
• Fix FileNotFoundError in get_reconstruction_output_metadata by @talonchandler in #510
• Add dependency license details by @talonchandler in #504
• Fix 3D phase unit consistency by @talonchandler in #511
• Non-integer focus support by @talonchandler in #473
• Run examples CI by @talonchandler in #513
• Backwards compatible stats from focus_from_transverse_band by @talonchandler in #512
• Update and test recon tab for pydantic v2 by @talonchandler in #514
• Update WaveOrder logo by @talonchandler in #516
• Hide acquisition tab by @talonchandler in #493
• Constrain PyQt6>=6.5,<6.8 for older linux systems by @talonchandler in #517

New Contributors

• @ahillsley made their first contribution in #445
• @amitabhverma made their first contribution in #458
• @tlambert03 made their first contribution in #477
• @srivarra made their first contribution in #508

Full Changelog: 2.2.1...3.0.0

3.0.0a3

What's Changed

• demos for AQLM 2025 by @mattersoflight in #446
• Updated to Pydantic V2 Models by @srivarra in #508
• Update is_single_position_store to catch FileNotFoundError by @talonchandler in #509
• Fix FileNotFoundError in get_reconstruction_output_metadata by @talonchandler in #510
• Add dependency license details by @talonchandler in #504
• Fix 3D phase unit consistency by @talonchandler in #511
• Non-integer focus support by @talonchandler in #473
• Run examples CI by @talonchandler in #513
• Backwards compatible stats from focus_from_transverse_band by @talonchandler in #512
• Update and test recon tab for pydantic v2 by @talonchandler in #514
• Update WaveOrder logo by @talonchandler in #516
• Hide acquisition tab by @talonchandler in #493
• Constrain PyQt6>=6.5,<6.8 for older linux systems by @talonchandler in #517

New Contributors

• @srivarra made their first contribution in #508

Full Changelog: 3.0.0a2...3.0.0a3

3.0.0a2

What's Changed

• Remove submitit dependency by @talonchandler in #454
• Skip reconstructions of empty FOVs by @ieivanov in #457
• Instructions to install from pip and github by @talonchandler in #451
• Gui update by @amitabhverma in #458
• Documentation infrastructure by @amitabhverma in #461
• Vector prototype CLI by @talonchandler in #440
• Refactor compute_midband_power by @talonchandler in #471
• run tests on pr by @tlambert03 in #477
• simplify test ci by @tlambert03 in #478
• tests: run example tests on ci and mock show by @tlambert03 in #476
• Exclude docs/, tests/, etc. from wheel by @talonchandler in #480
• Faster tests by @talonchandler in #487
• Handle single position .zarr stores as CLI input by @talonchandler in #486
• Fixes loading default phase.yml and fluorescence.yml config files in GUI by @amitabhverma in #488
• Improve installation instructions by @talonchandler in #479
• Package layout fix by @talonchandler in #489
• Visual assets appear in plugin by @talonchandler in #495
• Bump iohub by @talonchandler in #492
• 2D fluorescence reconstruction by @talonchandler in #460

New Contributors

• @amitabhverma made their first contribution in #458
• @tlambert03 made their first contribution in #477

Full Changelog: 3.0.0a1...3.0.0a2

3.0.0a1

What's Changed

• bug in monitor by @ahillsley in #445

New Contributors

• @ahillsley made their first contribution in #445

Full Changelog: 3.0.0a0...3.0.0a1

3.0.0a0

This release features the recOrder->waveorder merge and newly fixed 3D-to-2D phase reconstructions.

What's Changed

• Fix installation by @talonchandler in #184
• Fix style by @talonchandler in #185
• Fix pytests by @talonchandler in #186
• Clean up examples and temp files by @talonchandler in #187
• Remove recorder image references by @talonchandler in #189
• Merging README by @mattersoflight in #188
• Merge recOrder into waveorder by @talonchandler in #183
• Bump iohub and pydantic by @ziw-liu in #448
• Test on click 8.2.0 by @ziw-liu in #450
• Fix 3D to 2D phase reconstruction by @talonchandler in #441
• Settings-ratio checks should give warnings, not errors by @talonchandler in #452

Full Changelog: 2.2.1...3.0.0a0