.dockerignore
.gitignore
CLAUDE.md
CONTRIBUTING.md
LICENSE
README.md
codecov.yml
mkdocs.yml
pyproject.toml
uv.lock
.claude/commands/coverage.md
.claude/commands/lint.md
.claude/commands/pr-description.md
.claude/skills/investigation/SKILL.md
.claude/skills/pr/SKILL.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/build.yml
.github/workflows/ci.yml
.github/workflows/codespell.yml
.github/workflows/docs.yml
docs/index.md
docs/installation.md
docs/assets/favicon.ico
docs/assets/sleap-logo.png
docs/assets/sleap_movie.gif
docs/assets/images/bottomup_approach.png
docs/assets/images/topdown_approach.jpg
docs/configuration/data.md
docs/configuration/index.md
docs/configuration/model.md
docs/configuration/samples.md
docs/configuration/trainer.md
docs/configuration/config-picker/app.html
docs/configuration/config-picker/index.md
docs/getting-started/first-model.md
docs/getting-started/index.md
docs/getting-started/quickstart.md
docs/guides/config-generator.md
docs/guides/evaluation.md
docs/guides/export.md
docs/guides/index.md
docs/guides/inference.md
docs/guides/monitoring.md
docs/guides/multi-gpu.md
docs/guides/negative-frames.md
docs/guides/tracking.md
docs/guides/training.md
docs/help/faq.md
docs/reference/api.md
docs/reference/cli.md
docs/reference/evaluation_metrics.md
docs/reference/index.md
docs/reference/models.md
docs/sample_configs/config_bottomup_convnext.yaml
docs/sample_configs/config_bottomup_unet_large_rf.yaml
docs/sample_configs/config_bottomup_unet_medium_rf.yaml
docs/sample_configs/config_centroid_swint.yaml
docs/sample_configs/config_centroid_unet.yaml
docs/sample_configs/config_multi_class_bottomup_unet.yaml
docs/sample_configs/config_single_instance_unet_large_rf.yaml
docs/sample_configs/config_single_instance_unet_medium_rf.yaml
docs/sample_configs/config_topdown_centered_instance_unet_large_rf.yaml
docs/sample_configs/config_topdown_centered_instance_unet_medium_rf.yaml
docs/sample_configs/config_topdown_multi_class_centered_instance_unet.yaml
docs/stylesheets/extra.css
docs/tutorials/index.md
docs/tutorials/notebooks.md
example_notebooks/README.md
example_notebooks/augmentation_guide.py
example_notebooks/receptive_field_guide.py
example_notebooks/training_demo.py
scripts/cov_summary.py
scripts/gen_changelog.py
scripts/gen_ref_pages.py
sleap_nn/.DS_Store
sleap_nn/__init__.py
sleap_nn/cli.py
sleap_nn/evaluation.py
sleap_nn/legacy_models.py
sleap_nn/model_info.py
sleap_nn/predict.py
sleap_nn/system_info.py
sleap_nn/train.py
sleap_nn.egg-info/PKG-INFO
sleap_nn.egg-info/SOURCES.txt
sleap_nn.egg-info/dependency_links.txt
sleap_nn.egg-info/entry_points.txt
sleap_nn.egg-info/requires.txt
sleap_nn.egg-info/top_level.txt
sleap_nn/architectures/__init__.py
sleap_nn/architectures/common.py
sleap_nn/architectures/convnext.py
sleap_nn/architectures/encoder_decoder.py
sleap_nn/architectures/heads.py
sleap_nn/architectures/model.py
sleap_nn/architectures/swint.py
sleap_nn/architectures/unet.py
sleap_nn/architectures/utils.py
sleap_nn/config/__init__.py
sleap_nn/config/data_config.py
sleap_nn/config/get_config.py
sleap_nn/config/model_config.py
sleap_nn/config/trainer_config.py
sleap_nn/config/training_job_config.py
sleap_nn/config/utils.py
sleap_nn/config_generator/__init__.py
sleap_nn/config_generator/analyzer.py
sleap_nn/config_generator/generator.py
sleap_nn/config_generator/memory.py
sleap_nn/config_generator/recommender.py
sleap_nn/config_generator/tui/__init__.py
sleap_nn/config_generator/tui/app.py
sleap_nn/config_generator/tui/state.py
sleap_nn/config_generator/tui/screens/__init__.py
sleap_nn/config_generator/tui/screens/configure_screen.py
sleap_nn/config_generator/tui/screens/data_screen.py
sleap_nn/config_generator/tui/screens/export_screen.py
sleap_nn/config_generator/tui/screens/load_screen.py
sleap_nn/config_generator/tui/screens/model_screen.py
sleap_nn/config_generator/tui/screens/model_select_screen.py
sleap_nn/config_generator/tui/screens/topdown_screen.py
sleap_nn/config_generator/tui/screens/training_screen.py
sleap_nn/config_generator/tui/styles/app.tcss
sleap_nn/config_generator/tui/widgets/__init__.py
sleap_nn/config_generator/tui/widgets/collapsible.py
sleap_nn/config_generator/tui/widgets/info_box.py
sleap_nn/config_generator/tui/widgets/memory_gauge.py
sleap_nn/config_generator/tui/widgets/recommendation.py
sleap_nn/config_generator/tui/widgets/size_display.py
sleap_nn/config_generator/tui/widgets/slider.py
sleap_nn/data/__init__.py
sleap_nn/data/augmentation.py
sleap_nn/data/confidence_maps.py
sleap_nn/data/custom_datasets.py
sleap_nn/data/edge_maps.py
sleap_nn/data/identity.py
sleap_nn/data/instance_centroids.py
sleap_nn/data/instance_cropping.py
sleap_nn/data/normalization.py
sleap_nn/data/providers.py
sleap_nn/data/resizing.py
sleap_nn/data/skia_augmentation.py
sleap_nn/data/utils.py
sleap_nn/export/__init__.py
sleap_nn/export/cli.py
sleap_nn/export/inference.py
sleap_nn/export/metadata.py
sleap_nn/export/utils.py
sleap_nn/export/exporters/__init__.py
sleap_nn/export/exporters/onnx_exporter.py
sleap_nn/export/exporters/tensorrt_exporter.py
sleap_nn/export/predictors/__init__.py
sleap_nn/export/predictors/base.py
sleap_nn/export/predictors/onnx.py
sleap_nn/export/predictors/tensorrt.py
sleap_nn/export/wrappers/__init__.py
sleap_nn/export/wrappers/base.py
sleap_nn/export/wrappers/bottomup.py
sleap_nn/export/wrappers/bottomup_multiclass.py
sleap_nn/export/wrappers/centered_instance.py
sleap_nn/export/wrappers/centroid.py
sleap_nn/export/wrappers/single_instance.py
sleap_nn/export/wrappers/topdown.py
sleap_nn/export/wrappers/topdown_multiclass.py
sleap_nn/inference/__init__.py
sleap_nn/inference/bottomup.py
sleap_nn/inference/identity.py
sleap_nn/inference/paf_grouping.py
sleap_nn/inference/peak_finding.py
sleap_nn/inference/postprocessing.py
sleap_nn/inference/predictors.py
sleap_nn/inference/provenance.py
sleap_nn/inference/single_instance.py
sleap_nn/inference/topdown.py
sleap_nn/inference/utils.py
sleap_nn/tracking/__init__.py
sleap_nn/tracking/track_instance.py
sleap_nn/tracking/tracker.py
sleap_nn/tracking/utils.py
sleap_nn/tracking/candidates/__init__.py
sleap_nn/tracking/candidates/fixed_window.py
sleap_nn/tracking/candidates/local_queues.py
sleap_nn/training/__init__.py
sleap_nn/training/callbacks.py
sleap_nn/training/lightning_modules.py
sleap_nn/training/losses.py
sleap_nn/training/model_trainer.py
sleap_nn/training/schedulers.py
sleap_nn/training/utils.py
tests/__init__.py
tests/conftest.py
tests/test_cli.py
tests/test_evaluation.py
tests/test_legacy_models.py
tests/test_model_info.py
tests/test_parallel_caching.py
tests/test_predict.py
tests/test_system_info.py
tests/test_train.py
tests/test_version.py
tests/architectures/test_architecture_utils.py
tests/architectures/test_common.py
tests/architectures/test_convnext.py
tests/architectures/test_encoder_decoder.py
tests/architectures/test_heads.py
tests/architectures/test_model.py
tests/architectures/test_swint.py
tests/architectures/test_unet.py
tests/assets/datasets/centered_pair_small.mp4
tests/assets/datasets/minimal_instance.pkg.slp
tests/assets/datasets/small_robot.mp4
tests/assets/datasets/small_robot_minimal.slp
tests/assets/inference/minimal_bboxes.pt
tests/assets/inference/minimal_cms.pt
tests/assets/legacy_models/get_dummy_activations.py
tests/assets/legacy_models/min_tracks_2node.UNet.bottomup_multiclass/best_model.h5
tests/assets/legacy_models/min_tracks_2node.UNet.bottomup_multiclass/dummy_activations.h5
tests/assets/legacy_models/min_tracks_2node.UNet.bottomup_multiclass/initial_config.json
tests/assets/legacy_models/min_tracks_2node.UNet.bottomup_multiclass/training_config.json
tests/assets/legacy_models/min_tracks_2node.UNet.topdown_multiclass/best_model.h5
tests/assets/legacy_models/min_tracks_2node.UNet.topdown_multiclass/dummy_activations.h5
tests/assets/legacy_models/min_tracks_2node.UNet.topdown_multiclass/initial_config.json
tests/assets/legacy_models/min_tracks_2node.UNet.topdown_multiclass/training_config.json
tests/assets/legacy_models/minimal_instance.UNet.bottomup/best_model.h5
tests/assets/legacy_models/minimal_instance.UNet.bottomup/dummy_activations.h5
tests/assets/legacy_models/minimal_instance.UNet.bottomup/initial_config.json
tests/assets/legacy_models/minimal_instance.UNet.bottomup/labels_gt.train.slp
tests/assets/legacy_models/minimal_instance.UNet.bottomup/labels_gt.val.slp
tests/assets/legacy_models/minimal_instance.UNet.bottomup/labels_pr.train.slp
tests/assets/legacy_models/minimal_instance.UNet.bottomup/labels_pr.val.slp
tests/assets/legacy_models/minimal_instance.UNet.bottomup/metrics.train.npz
tests/assets/legacy_models/minimal_instance.UNet.bottomup/metrics.val.npz
tests/assets/legacy_models/minimal_instance.UNet.bottomup/training_config.json
tests/assets/legacy_models/minimal_instance.UNet.bottomup/training_log.csv
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/best_model.h5
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/dummy_activations.h5
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/initial_config.json
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/labels_gt.train.slp
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/labels_gt.val.slp
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/labels_pr.train.slp
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/labels_pr.val.slp
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/metrics.train.npz
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/metrics.val.npz
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/training_config.json
tests/assets/legacy_models/minimal_instance.UNet.centered_instance/training_log.csv
tests/assets/legacy_models/minimal_instance.UNet.centroid/best_model.h5
tests/assets/legacy_models/minimal_instance.UNet.centroid/dummy_activations.h5
tests/assets/legacy_models/minimal_instance.UNet.centroid/initial_config.json
tests/assets/legacy_models/minimal_instance.UNet.centroid/labels_gt.train.slp
tests/assets/legacy_models/minimal_instance.UNet.centroid/labels_gt.val.slp
tests/assets/legacy_models/minimal_instance.UNet.centroid/labels_pr.train.slp
tests/assets/legacy_models/minimal_instance.UNet.centroid/labels_pr.val.slp
tests/assets/legacy_models/minimal_instance.UNet.centroid/metrics.train.npz
tests/assets/legacy_models/minimal_instance.UNet.centroid/metrics.val.npz
tests/assets/legacy_models/minimal_instance.UNet.centroid/training_config.json
tests/assets/legacy_models/minimal_instance.UNet.centroid/training_log.csv
tests/assets/legacy_models/minimal_robot.UNet.single_instance/best_model.h5
tests/assets/legacy_models/minimal_robot.UNet.single_instance/dummy_activations.h5
tests/assets/legacy_models/minimal_robot.UNet.single_instance/initial_config.json
tests/assets/legacy_models/minimal_robot.UNet.single_instance/labels_gt.train.slp
tests/assets/legacy_models/minimal_robot.UNet.single_instance/labels_gt.val.slp
tests/assets/legacy_models/minimal_robot.UNet.single_instance/training_config.json
tests/assets/legacy_models/minimal_robot.UNet.single_instance/training_log.csv
tests/assets/legacy_sleap_json_configs/bottomup_multiclass_training_config.json
tests/assets/legacy_sleap_json_configs/bottomup_training_config.json
tests/assets/legacy_sleap_json_configs/centered_instance_training_config.json
tests/assets/legacy_sleap_json_configs/centered_instance_with_scaling_training_config.json
tests/assets/legacy_sleap_json_configs/centroid_training_config.json
tests/assets/legacy_sleap_json_configs/single_instance_training_config.json
tests/assets/legacy_sleap_json_configs/topdown_training_config.json
tests/assets/model_ckpts/minimal_instance_bottomup/best.ckpt
tests/assets/model_ckpts/minimal_instance_bottomup/initial_config.yaml
tests/assets/model_ckpts/minimal_instance_bottomup/labels_train_gt_0.slp
tests/assets/model_ckpts/minimal_instance_bottomup/labels_val_gt_0.slp
tests/assets/model_ckpts/minimal_instance_bottomup/training_config.yaml
tests/assets/model_ckpts/minimal_instance_bottomup/training_log.csv
tests/assets/model_ckpts/minimal_instance_centered_instance/best.ckpt
tests/assets/model_ckpts/minimal_instance_centered_instance/initial_config.yaml
tests/assets/model_ckpts/minimal_instance_centered_instance/labels_train_gt_0.slp
tests/assets/model_ckpts/minimal_instance_centered_instance/labels_val_gt_0.slp
tests/assets/model_ckpts/minimal_instance_centered_instance/training_config.yaml
tests/assets/model_ckpts/minimal_instance_centered_instance/training_log.csv
tests/assets/model_ckpts/minimal_instance_centroid/best.ckpt
tests/assets/model_ckpts/minimal_instance_centroid/initial_config.yaml
tests/assets/model_ckpts/minimal_instance_centroid/labels_train_gt_0.slp
tests/assets/model_ckpts/minimal_instance_centroid/labels_val_gt_0.slp
tests/assets/model_ckpts/minimal_instance_centroid/training_config.yaml
tests/assets/model_ckpts/minimal_instance_centroid/training_log.csv
tests/assets/model_ckpts/minimal_instance_multiclass_bottomup/best.ckpt
tests/assets/model_ckpts/minimal_instance_multiclass_bottomup/initial_config.yaml
tests/assets/model_ckpts/minimal_instance_multiclass_bottomup/labels_train_gt_0.slp
tests/assets/model_ckpts/minimal_instance_multiclass_bottomup/labels_val_gt_0.slp
tests/assets/model_ckpts/minimal_instance_multiclass_bottomup/training_config.yaml
tests/assets/model_ckpts/minimal_instance_multiclass_bottomup/training_log.csv
tests/assets/model_ckpts/minimal_instance_multiclass_centered_instance/best.ckpt
tests/assets/model_ckpts/minimal_instance_multiclass_centered_instance/initial_config.yaml
tests/assets/model_ckpts/minimal_instance_multiclass_centered_instance/labels_train_gt_0.slp
tests/assets/model_ckpts/minimal_instance_multiclass_centered_instance/labels_val_gt_0.slp
tests/assets/model_ckpts/minimal_instance_multiclass_centered_instance/training_config.yaml
tests/assets/model_ckpts/minimal_instance_multiclass_centered_instance/training_log.csv
tests/assets/model_ckpts/minimal_instance_single_instance/best.ckpt
tests/assets/model_ckpts/minimal_instance_single_instance/initial_config.yaml
tests/assets/model_ckpts/minimal_instance_single_instance/labels_train_gt_0.slp
tests/assets/model_ckpts/minimal_instance_single_instance/labels_val_gt_0.slp
tests/assets/model_ckpts/minimal_instance_single_instance/training_config.yaml
tests/assets/model_ckpts/minimal_instance_single_instance/training_log.csv
tests/assets/model_ckpts/single_instance_with_metrics/best.ckpt
tests/assets/model_ckpts/single_instance_with_metrics/initial_config.yaml
tests/assets/model_ckpts/single_instance_with_metrics/labels_train_gt_0.slp
tests/assets/model_ckpts/single_instance_with_metrics/labels_val_gt_0.slp
tests/assets/model_ckpts/single_instance_with_metrics/pred_test.slp
tests/assets/model_ckpts/single_instance_with_metrics/pred_train_0.slp
tests/assets/model_ckpts/single_instance_with_metrics/pred_val_0.slp
tests/assets/model_ckpts/single_instance_with_metrics/test_pred_metrics.npz
tests/assets/model_ckpts/single_instance_with_metrics/train_0_pred_metrics.npz
tests/assets/model_ckpts/single_instance_with_metrics/training_config.yaml
tests/assets/model_ckpts/single_instance_with_metrics/training_log.csv
tests/assets/model_ckpts/single_instance_with_metrics/val_0_pred_metrics.npz
tests/config/test_config_utils.py
tests/config/test_data_config.py
tests/config/test_model_config.py
tests/config/test_trainer_config.py
tests/config/test_training_job_config.py
tests/data/test_augmentation.py
tests/data/test_confmaps.py
tests/data/test_custom_datasets.py
tests/data/test_edge_maps.py
tests/data/test_identity.py
tests/data/test_instance_centroids.py
tests/data/test_instance_cropping.py
tests/data/test_negative_frames.py
tests/data/test_normalization.py
tests/data/test_providers.py
tests/data/test_resizing.py
tests/data/test_utils.py
tests/export/__init__.py
tests/export/conftest.py
tests/export/test_cli.py
tests/export/test_export_accuracy.py
tests/export/test_gpu.py
tests/export/test_inference.py
tests/export/test_metadata.py
tests/export/test_onnx_export.py
tests/export/test_onnx_predictor.py
tests/export/test_predictor_factory.py
tests/export/test_utils.py
tests/export/test_wrappers.py
tests/fixtures/__init__.py
tests/fixtures/datasets.py
tests/fixtures/inference.py
tests/fixtures/legacy_models.py
tests/fixtures/legacy_sleap_json_configs.py
tests/fixtures/model_ckpts.py
tests/fixtures/predictors.py
tests/inference/__init__.py
tests/inference/test_bottomup.py
tests/inference/test_paf_grouping.py
tests/inference/test_peak_finding.py
tests/inference/test_postprocessing.py
tests/inference/test_predictors.py
tests/inference/test_provenance.py
tests/inference/test_single_instance.py
tests/inference/test_topdown.py
tests/inference/test_utils.py
tests/tracking/test_tracker.py
tests/tracking/candidates/test_fixed_window.py
tests/tracking/candidates/test_local_queues.py
tests/training/test_callbacks.py
tests/training/test_lightning_modules.py
tests/training/test_model_trainer.py
tests/training/test_schedulers.py
tests/training/test_training_utils.py