What's Changed

• Fix PySide6 AttributeError and uninitialized variable by @jeylau in #2622
• Niels/pcutoff arg by @n-poulsen in #2630
• Fix video overwrite by @jeylau in #2633
• Visually signal end of super animal video inference by @jeylau in #2637
• Fix GUI bugs by @jeylau in #2649
• Fix OSError: Could not find a backend to open CollectedData_Alex.csv with iomode r by @jeylau in #2650
• Fix video extension filter in filterpredictions by @jeylau in #2673
• Fix and decouple video rotation from other operations by @jeylau in #2653
• merge named snapshot evaluation into pytorch_dlc by @n-poulsen in #2657
• Handle internet connectivity issues by @jeylau in #2672
• New PyTorch DeepLabCut SuperAnimal demo notebook by @yeshaokai in #2629
• merge main to pytorch_dlc by @n-poulsen in #2677
• Update train.py: avoids error on 'unique_bodyparts' by @Zelin2001 in #2668
• Default PAF config update by @n-poulsen in #2678
• New detector options and better detector integration by @n-poulsen in #2676
• backwards compatibility by @n-poulsen in #2681
• evaluation refactor by @n-poulsen in #2679
• bug fixes for analyze_videos and unique_bodyparts by @Zelin2001 in #2685
• Fix import in deeplabcut.pose_tracking_pytorch by @jeylau in #2691
• Location Refinement for Top-Down models by @n-poulsen in #2699
• Identity Predictor by @n-poulsen in #2707
• batched inference by @n-poulsen in #2708
• Bug fixes: find_closest_neighbors + ellipse tracking by @n-poulsen in #2709
• bug fix: find closest neighbors by @n-poulsen in #2717
• Minimal backward compatibility by @AlexEMG in #2713
• Documentation Improvements - DeepLabCut PyTorch Code by @AlexEMG in #2714
• merge main into pytorch_dlc by @n-poulsen in #2731
• Make 3D Triangulate possible with pytorch_dlc branch and MA project by @Zelin2001 in #2729
• Data compatibility - Benchmark by @n-poulsen in #2740
• Adding cropping to pose_estimation_pytorch/apis/analyze_videos.py by @YankoFelipe in #2737
• pytorch_dlc - Small updates and bug fixes by @n-poulsen in #2747
• calc_similarity_with .py ZeroDivisionError: float division by zeros via upload by @SowonKIMM in #2688
• update version by @AlexEMG in #2748
• SuperAnimal Model Updates by @n-poulsen in #2756
• Look for uppercase video extensions when creating projects by @n-poulsen in #2763
• Fix reading gpus config by @maximpavliv in #2764
• Git ignore IDE configs by @maximpavliv in #2765
• Fix bug introduced in PR #2764 by @maximpavliv in #2772
• Bug fix: create_video_with_all_detections fails with PAF heads by @n-poulsen in #2776
• Resume training from existing snapshots option in GUI by @maximpavliv in #2774
• Improvements to the training UX by @n-poulsen in #2775
• Fix failing DLC 3.0 tests - changes to internal implementation by @n-poulsen in #2778
• Merge changes made to main by @n-poulsen in #2779
• Fix: gui/tabs/train_network.py, AttributeError: ‘NoneType’ object has no attribute ‘lower’ by @n-poulsen in #2780
• Use architecture-specific snapshots prefixes in video adaptation by @maximpavliv in #2781
• Video Analysis with Identity - Lowering memory footprint by @n-poulsen in #2785
• Timeout retrieving latest package version from the Web by @maximpavliv in #2782
• Load scheduler state when resuming training by @n-poulsen in #2788
• DeepLabCut 3.0 - Video Analysis with use_shelve=True by @n-poulsen in #2790
• Fix: correct the early return error when save_epochs=1 and optimize the clean up way by @xiu-cs in #2793
• Fix: Video Analysis for Single Animal projects by @n-poulsen in #2798
• Model Output Visualization for PyTorch Models by @n-poulsen in #2799
• Add Functions for Visualizing COCO Predictions and Ground Truth by @xiu-cs in #2792
• DLC 3.0 - Function to export PyTorch models by @n-poulsen in #2800
• KeypointAwareCrop: uniform sampling when no keypoints are present by @n-poulsen in #2801
• Fix version check timeout by @maximpavliv in #2805
• Revert "Fix version check timeout" by @n-poulsen in #2807
• PyTorch model evaluation - per_keypoint_evaluation and comparisonbodyparts by @n-poulsen in #2810
• Prune PAF graphs before evaluation by @n-poulsen in #2813
• Plot detector's bboxes if Top-Down architecture by @maximpavliv in #2791
• superanimal_analyze_images: improve plotting functions by @n-poulsen in #2815
• Update superanimal_analyze_images plotting by @n-poulsen in #2817
• Set weights_only=True as a default when loading snapshot weights. by @n-poulsen in #2818
• Implement missing arguments for PyTorch models by @n-poulsen in #2816
• Add missing positional arguments to SuperAnimal Colab by @maximpavliv in #2819
• New Top-Down Pose Estimation Model - RTMPose by @n-poulsen in #2795
• SuperAnimal demo colab update (for DLC3) by @MMathisLab in #2814
• Improved loading of snapshot weights with torch.load(..., weights_only=True) by @MMathisLab in #2823
• create_labeled_video fails with single animal TensorFlow models by @n-poulsen in #2826
• Merges main into pytorch_dlc by @n-poulsen in #2828
• Restore "Build skeleton" button by @maximpavliv in #2831
• Improve deeplabcut.pose_estimation_pytorch imports by @n-poulsen in #2833
• Improve train_network() docstring by @maximpavliv in #2836
• get_detector_inference_runner: resolve the device from the model config when None by @nattse in #2841
• Update docs video_inference_superanimal() by @maximpavliv in #2848
• Fix - setting cropping parameters in analyze_videos for PyTorch models by @n-poulsen in #2849
• Improvements to default configs by @n-poulsen in #2860
• Dynamic update of pytorch config with dot notation by @maximpavliv in #2859
• fix broken train_network argument display_iters in the GUI by @n-poulsen in #2865
• ReID Tracking dataset creation for PyTorch models by @n-poulsen in #2861
• Merges main into pytorch_dlc by @maximpavliv in #2876
• fix evaluation for ma models, following change in 'deeplabcut/core/metrics/api.py' by @Zelin2001 in #2872
• Fix check version timeout Version 2 (compatible with Windows and MacOS) by @maximpavliv in #2820
• fix entrypoint for dlc by @hmaarrfk in #2863
• Fix entrypoint - Requested changes by @maxi...

What's Changed

• Update beginners-guide.md by @MMathisLab in #2619
• Update DEEPLABCUT.yaml by @EitanHemed in #2625
• Add feature to evaluate network for specfic, named snapshots. by @Tetra-quark in #2508
• fixed file dialog not showing uppercase file extension video files by @park-jsdev in #2645
• Swap button added to the track refinement GUI by @JulianAlvarezdeGiorgi in #2680
• Fixes for testscript_3d.py by @jesse-gilmer in #2443
• Allow processing of videos in MKV containers by @ximion in #2701
• add in CZI EOSS badge and funding section by @MMathisLab in #2735
• Fix minimalnumberofconnections by @segashin in #2718
• Benchmarking user guide by @dikraMasrour in #2716
• adding docs for using data labeled elsewhere (formatting) by @MMathisLab in #2736
• Update standardDeepLabCut_UserGuide.md by @bendichter in #2761
• Create citation.md by @MMathisLab in #2767
• Fix failing tests - tmpdir_factory dir creation on OSX by @n-poulsen in #2768
• Update DLC3 PyTorch docs by @n-poulsen in #2804
• Pins numpy<2, fix svd for scipy>=1.11.0 by @n-poulsen in #2827
• Fix reading filtered state by @maximpavliv in #2844
• Remove pickle5 dependency from madlc Colab by @maximpavliv in #2846
• Fixed dropimagesduetolackofannotation to work with single-animal data by @n-poulsen in #2850
• Fixed conversion of dict to list for proper future indexing by @m-beau in #2855
• fixes to label_frames, addition of docstring by @n-poulsen in #2858
• Pin TensorFlow according to OS; Fix DeepLabCut install in Colab to deal with new requirements. by @n-poulsen in #2862
• Remove unused GUI button in analyze videos tab by @maximpavliv in #2875
• Fix video addition in VideoSelectionWidget by @maximpavliv in #2878
• v2.3.11 by @AlexEMG in #2882
• improved handling of animal names when analyzing videos by @n-poulsen in #2884

New Contributors

• @park-jsdev made their first contribution in #2645
• @JulianAlvarezdeGiorgi made their first contribution in #2680
• @jesse-gilmer made their first contribution in #2443
• @ximion made their first contribution in #2701
• @segashin made their first contribution in #2718
• @dikraMasrour made their first contribution in #2716
• @bendichter made their first contribution in #2761
• @m-beau made their first contribution in #2855

@maximpavliv joined the software team!

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Full Changelog: v2.3.10...v2.3.11

What's Changed

• Doc re-arrangement in the TOC by @MMathisLab in #2523
• slight change to setup (move all TF to TF tag; pin tables, add note that python 3.9 is currently required by @MMathisLab in #2517
• Use video crop coordinates appropriately in create_video_with_all_detections by @jeylau in #2524
• Avoid infinite loop in mine() when there are no overlapping tracklets by @jeylau in #2525
• fix manual frame extraction with symlinks by @n-poulsen in #2527
• Update COLAB_DLC_ModelZoo.ipynb by @MMathisLab in #2533
• Adding a Quick Guide (from the wiki to the docs!) by @MMathisLab in #2532
• quick file fix by @MMathisLab in #2534
• Update installTips.md by @MMathisLab in #2536
• Video analysis on cropped videos: bug fixes for extract_outlier_frames and create_video_with_all_detections by @n-poulsen in #2538
• MacOS CI Fix - FFMpeg Installation by @n-poulsen in #2559
• niels/check_for_duplicate_videos by @n-poulsen in #2558
• Update setup.py by @MMathisLab in #2526
• bug fix: missing images during evaluation by @n-poulsen in #2570
• Update label and warn users of the absence of videos by @jeylau in #2586
• pin matplotlib version by @n-poulsen in #2583
• Correct DEEPLABCUT.yaml and DEEPLABCUT_M1.yaml reference. by @midumitrescu in #2573
• minor spelling fixes by @MMathisLab in #2594
• Fix 2d line data setter by @jeylau in #2599
• Auto check for dlclibrary & napari-deeplabcut updates when the GUI opens by @jeylau in #2600
• Update README.md by @MMathisLab in #2601
• Release by @AlexEMG in #2602

New Contributors

• @midumitrescu made their first contribution in #2573

Full Changelog: v2.3.9...v2.9.10

• Add GUI help button back by @jeylau in #2507

What's Changed

• Pull demo data from Zenodo by @jeylau in #2440
• Update maDLC_UserGuide.md by @Timokleia in #2446
• Fix bug dataset and metadataset fixes #2390 by @Tetra-quark in #2405
• Bug fix: add_new_videos(..., extract_frames=True) by @n-poulsen in #2468
• bug fix: empty predictions during video analysis by @n-poulsen in #2467
• Update README.md by @MMathisLab in #2464
• Update AUTHORS by @MMathisLab in #2475
• updated macOS runner to 13 by @n-poulsen in #2484
• Update README.md by @Timokleia in #2496
• Bump version of tables installed during CI by @jeylau in #2500
• updated COLAB notebooks to install a CUDA version compatible with DLC by @n-poulsen in #2506
• updated package requirements by @n-poulsen in #2513
• Test for the presence of snapshot files when using modelzoo by @jeylau in #2485
• Version update by @AlexEMG in #2514

Full Changelog: v2.3.8...v2.3.9

What's Changed

• better augmentation for maDLC: Fix fliplr augmentation for multi animal 2 by @biol-jsh in #2043
• Improved transfer learning for DLC ModelZoo by @yeshaokai in #2389
• Improvements to the model zoo's GUI tab by @jeylau in #2431
• "deeplabcut.filterpredictions" and "deeplabcut.analyze_skeleton" return mappings by @rahulporuri in #1908
• Let user change the search window size during corner detection refinement by @jeylau in #2414
• Install DLC from PyPI rather than its local version in M1 Macs by @jeylau in #2416
• Correct link to platform specifications page by @molecules in #2423
• Automatically check for napari-deeplabcut updates (in addition to DLC) by @jeylau in #2422
• Smartly restore pretrained model weights by @jeylau in #2426
• Fix video adaptation by @jeylau in #2436

New Contributors

• @molecules made their first contribution in #2423

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Full Changelog: v2.3.7...v2.3.8

What's Changed

• update the lr when switching to adam optimizer by @n-poulsen in #2393
• Update maDLC_UserGuide.md by @Timokleia in #2394
• Fix testscript.py execution: set max_iters when training network by @n-poulsen in #2395
• Update python-package.yml by @MMathisLab in #2401
• Bump python to 3.9 in DEEPLABCUT.yaml environment file by @jeylau in #2402
• Address underlying compatibility issue with scipy 1.11.0 by @hmaarrfk in #2396
• Update standardDeepLabCut_UserGuide.md by @MMathisLab in #2403
• Unifying docs on Napari DeepLabCut by @Timokleia in #2399
• Update publish-book.yml by @MMathisLab in #2404
• Napari Flowchart by @Timokleia in #2406
• Minor modifications to deploy_book github action by @jeylau in #2407
• Update URL of napari shortcuts SVG by @jeylau in #2408
• update notebooks and COLAB by @n-poulsen in #2411
• GUI - Fix config YAML edition (start list indexing at 0) by @n-poulsen in #2412
• Fix link typos and conversion by @AlexEMG in #2409
• Update version by @AlexEMG in #2413

Full Changelog: v2.3.6...v2.3.7

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

What's Changed

• Fix deprecated numpy builtin type by @jeylau in #2270
• Fix display bodyparts by @KonradDanielewski in #2264
• fix drawing of skeleton when displayedbodyparts != all by @KonradDanielewski in #2274
• stitch_tracklets crashes when not enough tracks are found by @n-poulsen in #2273
• Pass train/test indices to create_multianimaltraining_dataset by @jeylau in #2272
• renamed attempttomakefolder to attempt_to_make_folder by @rizarae-p in #2271
• pin scipy to less than 1.11.0 by @n-poulsen in #2290
• Fixed draw_bbox when pyplot is in non-interactive mode by @n-poulsen in #2288
• Bug fix spatiotemporal adaptation kwargs by @n-poulsen in #2291
• Update README.md by @MMathisLab in #2294
• Avoid creating training dataset with multiple scorers by @KonradDanielewski in #2287
• handles empty frame in video adaptation by @yeshaokai in #2258
• Update DEEPLABCUT.yaml by @MMathisLab in #2299
• pinned tensorflow to <2.13.0 by @n-poulsen in #2308
• Manual outlier_frame_extraction bugfix by @n-poulsen in #2307
• Fix windows video selection for extraction in the GUI by @KonradDanielewski in #2286
• Add function to get per-bodypart RMSE by @n-poulsen in #2315
• Plot keypoint confidence as alpha value by @n-poulsen in #2319
• Some usability improvements to the main GUI by @jeylau in #2275
• fix broken gputouse by @ludovicbellier in #2320
• Avoid assembling if already done and overwrite == False by @KonradDanielewski in #2317
• Pose_cfg.yaml recipe by @KonradDanielewski in #2331
• Add link to hyperparams/augmentation guide by @KonradDanielewski in #2333
• Update DEEPLABCUT.yaml by @MMathisLab in #2325
• bug fix: assemblies filename print by @n-poulsen in #2346
• Fixed analyze_videos docstring by @n-poulsen in #2354
• ortholonal -> orthogonal by @yowayb in #2368
• Do not unpickle unit test data with pandas by @jeylau in #2373
• Updated deeplabcut installation in colab notebooks by @n-poulsen in #2376
• Added a new recipe on how to publish new recipes by @rizarae-p in #2334
• Remove unused parameter num_shuffles from check_for_weights function. by @Tetra-quark in #2360
• Update installation.md by @MMathisLab in #2378
• Update installation.md by @MMathisLab in #2379
• updated Model Zoo Colab notebook by @MMathisLab in #2381
• Doc clean up by @MMathisLab in #2380
• Clean up Model Zoo superanimal notebook by @MMathisLab in #2382
• Fix interp kwarg in imresize function. by @Tetra-quark in #2374
• Add build matrix for docker images, update images by @stes in #1936
• Update UseOverviewGuide and docker guide by @MMathisLab in #2384
• Update README.md by @MMathisLab in #2385
• Bug fixes VideoWriter: video names with spaces by @n-poulsen in #2388
• Branch for new version by @AlexEMG in #2392

New Contributors

• @rizarae-p made their first contribution in #2271
• @yowayb made their first contribution in #2368
• @Tetra-quark made their first contribution in #2360

Full Changelog: v2.3.5...v2.3.6

What's Changed

• Fetch mice demo data from Zenodo by @jeylau in #2223
• Changing except Error type to match no files found by @nattse in #2226
• Fix randomly failing multi-animal test script by @jeylau in #2233
• Fix rectangle selector by @n-poulsen in #2227
• Moved sections from H3 to H2 by @aoot in #2231
• removed deprecated install tips for mac m1/m2 by @n-poulsen in #2234
• Fix docstring in video_inference_superanimal by @stes in #2236
• 4 additional unit-tests by @AlexEMG in #2239
• Update URL for deeplabcut-docker by @stes in #2249
• Update bug_report.yml by @MMathisLab in #2250
• Allow frame extraction on a video subset in GUI by @jeylau in #2238
• Basicformatting by @AlexEMG in #2241
• Explicitely use QRegularExpression instead of implicit string conversion by @hmaarrfk in #2244
• Use QFrame.Shape.StyledPanel instead of QFrame.StyledPanel by @hmaarrfk in #2243
• Update use of .Directory for PySide6.5.0 by @hmaarrfk in #2247
• Additions to modelzoo APIs by @yeshaokai in #2198
• Update setup.py, docs by @MMathisLab in #2255
• version update by @AlexEMG in #2257

New Contributors

• @nattse made their first contribution in #2226
• @n-poulsen made their first contribution in #2227
• @aoot made their first contribution in #2231

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

Full Changelog: v2.3.4...v2.3.5

What's Changed

• Fix model zoo video adaptation by @jeylau in #2181
• GUI fixes by @KonradDanielewski in #2126
• Guarantee tracks are sorted by predicted identity by @jeylau in #2194
• Improved thread-safety of tracklet refinement GUI by @jeylau in #2191
• Catch ValueError when tracklet dict is empty by @jeylau in #2189
• Copy rather than move video files when symlink creation fails by @jeylau in #2187
• Auto default to ellipse in create_labeled_video for multi-animal projects by @jeylau in #2188
• Fix deprecated features in pandas 2.0 by @jeylau in #2160
• Update installation.md by @MMathisLab in #2214
• Fix AttributeError in Analyze Video tab with single animal projects by @jeylau in #2210
• Fix ArtistList's AttributeError by @jeylau in #2216
• Update multiple_individuals_trainingsetmanipulation.py by @MMathisLab in #2219
• codespell: config, action and a few typos fixed by @yarikoptic in #2217
• Fix typo in refine_tracklets.py by @xun468 in #2221
• v2.3.4 -- Update version for release by @AlexEMG in #2222

New Contributors

• @yarikoptic made their first contribution in #2217
• @xun468 made their first contribution in #2221

Full Changelog: v2.3.2...v2.3.4

Funding includes ChanZuckerberg Initiative's Essential Open Source Software for Science. Thanks!

This release note summarizes changes in v2.3.1 and 2.3.2 jointly.

What's Changed

• improve model zoo install and docs by @MMathisLab in #2105
• depreciated modelzoo urls by @MMathisLab in #2113
• Auto-load video and data when manually extracting outliers by @jeylau in #2114
• Fix typo by @jeylau in #2119
• Better handling failures in video creating GUI by @kngwyu in #2075
• Fix typo in add_new_videos function documentation. by @rojasgabriel in #2129
• Fix typo by @jeylau in #2135
• Add warning message during calibration when no complete poses are found by @jeylau in #2131
• extracted defs from main functions by @xarisot in #2122
• Label video when num_outputs > 1 (and overwriting flag) by @ludovicbellier in #2096
• Fix keypoint location in create_labeled_video after cropped analysis by @jeylau in #2147
• Fix typo in argument given to GUI's deeplabcut.filterpredictions by @jeylau in #2148
• Refine manual frames by @jonahpearl in #2045
• pin torch to less than 1.12 by @MMathisLab in #2156
• Model Zoo new API by @MMathisLab in #2109
• V2.3.1 by @AlexEMG in #2168
• Add missing data file in setup.py by @jeylau in #2170
• Update README.md by @MMathisLab in #2175
• v232 by @AlexEMG in #2176

New Contributors

• @rojasgabriel made their first contribution in #2129
• @xarisot made their first contribution in #2122
• @jonahpearl made their first contribution in #2045

Full Changelog: v2.3...v2.3.2