Releases · DeepLabCut/DeepLabCut

v3.0.0rc10

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

v2.3.10

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

Updates and bug fixes

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

Expanded GUI features for the DLC ModelZoo

Minor fixes

Bug fixes and minor updates

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

v2.3.5

Minor updates and bug fixes

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

v3.0.0rc10

What's Changed

v2.3.11 🐛 fixes, package maintenance (TF only)

What's Changed

New Contributors

v2.3.10

What's Changed

New Contributors

Updates and bug fixes

What's Changed

Expanded GUI features for the DLC ModelZoo

Minor fixes

Bug fixes and minor updates

What's Changed

New Contributors

v2.3.5

Minor updates and bug fixes

Minor updates and bug fixes

What's Changed

New Contributors