sleap-nn 0.1.0a2__tar.gz → 0.1.0a4__tar.gz

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/.github/workflows/docs.yml

@@ -57,7 +57,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-            uv run mike deploy --allow-empty --push "${{ github.event.release.tag_name }}"
+            uv run mike deploy --update-aliases --allow-empty --push "${{ github.event.release.tag_name }}" prerelease
 
       - name: Build and upload docs (dev)
         if: ${{ github.event_name == 'push' }}

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sleap-nn
-Version: 0.1.0a2
+Version: 0.1.0a4
 Summary: Neural network backend for training and inference for animal pose estimation.
 Author-email: Divya Seshadri Murali <dimurali@salk.edu>, Elizabeth Berrigan <eberrigan@salk.edu>, Vincent Tu <vitu@ucsd.edu>, Liezl Maree <lmaree@salk.edu>, David Samy <davidasamy@gmail.com>, Talmo Pereira <talmo@salk.edu>
 License: BSD-3-Clause
@@ -32,6 +32,7 @@ Requires-Dist: hydra-core
 Requires-Dist: jupyter
 Requires-Dist: jupyterlab
 Requires-Dist: pyzmq
+Requires-Dist: rich-click>=1.9.5
 Provides-Extra: torch
 Requires-Dist: torch; extra == "torch"
 Requires-Dist: torchvision>=0.20.0; extra == "torch"
@@ -47,6 +48,17 @@ Requires-Dist: torchvision>=0.20.0; extra == "torch-cuda128"
 Provides-Extra: torch-cuda130
 Requires-Dist: torch; extra == "torch-cuda130"
 Requires-Dist: torchvision>=0.20.0; extra == "torch-cuda130"
+Provides-Extra: export
+Requires-Dist: onnx>=1.15.0; extra == "export"
+Requires-Dist: onnxruntime>=1.16.0; extra == "export"
+Requires-Dist: onnxscript>=0.1.0; extra == "export"
+Provides-Extra: export-gpu
+Requires-Dist: onnx>=1.15.0; extra == "export-gpu"
+Requires-Dist: onnxruntime-gpu>=1.16.0; extra == "export-gpu"
+Requires-Dist: onnxscript>=0.1.0; extra == "export-gpu"
+Provides-Extra: tensorrt
+Requires-Dist: tensorrt>=10.0.0; extra == "tensorrt"
+Requires-Dist: torch-tensorrt>=2.0.0; extra == "tensorrt"
 Dynamic: license-file
 
 # sleap-nn

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/docs/cli.md

@@ -9,6 +9,8 @@ This page provides a quick reference for all `sleap-nn` command-line interface (
 | [`sleap-nn train`](#sleap-nn-train) | Train pose estimation models | [Training Guide](training.md) |
 | [`sleap-nn track`](#sleap-nn-track) | Run inference and/or tracking | [Inference Guide](inference.md) |
 | [`sleap-nn eval`](#sleap-nn-eval) | Evaluate predictions against ground truth | [Inference Guide](inference.md#evaluation-metrics) |
+| [`sleap-nn export`](#sleap-nn-export) | Export models to ONNX/TensorRT | [Export Guide](export.md) |
+| [`sleap-nn predict`](#sleap-nn-predict) | Run inference on exported models | [Export Guide](export.md#sleap-nn-predict) |
 | [`sleap-nn system`](#sleap-nn-system) | Display system info and GPU diagnostics | - |
 
 ## Global Options
@@ -170,6 +172,14 @@ sleap-nn track -i labels.slp -t
 | `--integral_refinement` | Refinement method (`integral` or `None`) | `integral` |
 | `--integral_patch_size` | Patch size for integral refinement | `5` |
 
+#### Filtering Overlapping Instances
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `--filter_overlapping` | Enable filtering of overlapping instances | `False` |
+| `--filter_overlapping_method` | Similarity method: `iou` (bbox) or `oks` (keypoints) | `iou` |
+| `--filter_overlapping_threshold` | Similarity threshold (higher = less filtering) | `0.8` |
+
 #### Tracking Options
 
 | Option | Description | Default |
@@ -256,6 +266,98 @@ See [Evaluation Metrics](inference.md#evaluation-metrics) for more details.
 
 ---
 
+## `sleap-nn export`
+
+!!! warning "Experimental"
+    This command is experimental. See the [Export Guide](export.md) for details.
+
+Export trained models to ONNX and/or TensorRT format for optimized inference.
+
+```bash
+sleap-nn export MODEL_PATH [MODEL_PATH_2] -o OUTPUT_DIR [options]
+```
+
+### Arguments
+
+| Argument | Description |
+|----------|-------------|
+| `MODEL_PATH` | Path to trained model checkpoint directory |
+| `MODEL_PATH_2` | Second model path for top-down (centroid + instance) |
+
+### Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--output-dir` | `-o` | Output directory for exported models | Required |
+| `--format` | `-f` | Export format: `onnx`, `tensorrt`, or `both` | `onnx` |
+| `--precision` | | TensorRT precision: `fp32` or `fp16` | `fp16` |
+| `--max-instances` | `-n` | Maximum instances per frame | `20` |
+| `--max-batch-size` | `-b` | Maximum batch size for dynamic shapes | `8` |
+| `--input-scale` | | Input resolution scale factor | `1.0` |
+| `--device` | | Device for export: `cuda` or `cpu` | `cuda` |
+
+### Examples
+
+```bash
+# Export single model to ONNX
+sleap-nn export models/single_instance -o exports/model --format onnx
+
+# Export to both ONNX and TensorRT
+sleap-nn export models/bottomup -o exports/model --format both
+
+# Export top-down (combined centroid + instance)
+sleap-nn export models/centroid models/centered_instance -o exports/topdown
+```
+
+See [Export Guide](export.md) for detailed documentation.
+
+---
+
+## `sleap-nn predict`
+
+!!! warning "Experimental"
+    This command is experimental. See the [Export Guide](export.md) for details.
+
+Run inference on exported ONNX/TensorRT models.
+
+```bash
+sleap-nn predict EXPORT_DIR INPUT_PATH [options]
+```
+
+### Arguments
+
+| Argument | Description |
+|----------|-------------|
+| `EXPORT_DIR` | Path to exported model directory |
+| `INPUT_PATH` | Path to video file |
+
+### Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--output` | `-o` | Output path for predictions (`.slp`) | `<input>.predictions.slp` |
+| `--runtime` | `-r` | Runtime: `auto`, `onnx`, or `tensorrt` | `auto` |
+| `--batch-size` | `-b` | Inference batch size | `4` |
+| `--n-frames` | `-n` | Number of frames to process (0 = all) | `0` |
+| `--device` | | Device: `auto`, `cuda`, or `cpu` | `auto` |
+
+### Examples
+
+```bash
+# Basic inference with auto-detected runtime
+sleap-nn predict exports/model video.mp4 -o predictions.slp
+
+# Use TensorRT for maximum speed
+sleap-nn predict exports/model video.mp4 -o predictions.slp --runtime tensorrt
+
+# Process first 1000 frames with batch size 8
+sleap-nn predict exports/model video.mp4 -o predictions.slp -n 1000 -b 8
+```
+
+See [Export Guide](export.md#sleap-nn-predict) for detailed documentation.
+
+---
+
 ## `sleap-nn system`
 
 Display system information and GPU diagnostics. Useful for troubleshooting GPU issues and verifying your installation.
@@ -310,3 +412,4 @@ This command is particularly helpful when:
 - [Configuration Guide](config.md) - Full config reference
 - [Training Guide](training.md) - Detailed training documentation
 - [Inference Guide](inference.md) - Detailed inference documentation
+- [Export Guide](export.md) - Model export and fast inference

sleap_nn-0.1.0a4/docs/export.md

@@ -0,0 +1,431 @@
+# Model Export and Fast Inference
+
+!!! warning "Experimental Feature"
+    The export module is **experimental** and under active development. APIs and behavior may change in future releases. Please report issues at [github.com/talmolab/sleap-nn/issues](https://github.com/talmolab/sleap-nn/issues).
+
+This guide covers exporting trained SLEAP models to optimized formats (ONNX and TensorRT) for high-performance inference without the full training environment.
+
+## Overview
+
+The export module provides:
+
+- **ONNX export** - Portable models that run on any platform with ONNX Runtime
+- **TensorRT export** - Maximum performance on NVIDIA GPUs with FP16 optimization
+- **Unified prediction CLI** - Run inference on exported models with SLP output
+
+### When to Use Exported Models
+
+| Use Case | Recommended Format |
+|----------|-------------------|
+| Cross-platform deployment | ONNX |
+| Maximum GPU throughput | TensorRT FP16 |
+| CPU-only inference | ONNX |
+| Embedding in applications | ONNX or TensorRT |
+| Production pipelines | TensorRT FP16 |
+
+### Performance Comparison
+
+Benchmarks on **NVIDIA RTX A6000** (48 GB).
+
+**Batch size 1** (latency-optimized):
+
+| Model Type | Resolution | PyTorch | ONNX-GPU | TensorRT FP16 | Speedup |
+|------------|------------|---------|----------|---------------|---------|
+| Single Instance | 192×192 | 1.8 ms | 1.3 ms | 0.31 ms | 5.9x |
+| Centroid | 1024×1024 | 2.5 ms | 2.7 ms | 0.77 ms | 3.2x |
+| Top-Down | 1024×1024 | 11.4 ms | 9.7 ms | 2.31 ms | 4.9x |
+| Bottom-Up | 1024×1280 | 12.3 ms | 9.6 ms | 2.52 ms | 4.9x |
+| Multiclass Top-Down | 1024×1024 | 8.3 ms | 9.1 ms | 1.84 ms | 4.5x |
+| Multiclass Bottom-Up | 1024×1024 | 9.4 ms | 9.4 ms | 2.64 ms | 3.6x |
+
+**Batch size 8** (throughput-optimized):
+
+| Model Type | Resolution | PyTorch | ONNX-GPU | TensorRT FP16 | Speedup |
+|------------|------------|---------|----------|---------------|---------|
+| Single Instance | 192×192 | 3,111 FPS | 3,165 FPS | 11,039 FPS | 3.5x |
+| Centroid | 1024×1024 | 453 FPS | 474 FPS | 1,829 FPS | 4.0x |
+| Top-Down | 1024×1024 | 94 FPS | 122 FPS | 525 FPS | 5.6x |
+| Bottom-Up | 1024×1280 | 113 FPS | 121 FPS | 524 FPS | 4.6x |
+| Multiclass Top-Down | 1024×1024 | 127 FPS | 145 FPS | 735 FPS | 5.8x |
+| Multiclass Bottom-Up | 1024×1024 | 116 FPS | 120 FPS | 470 FPS | 4.1x |
+
+*Speedup is relative to PyTorch baseline.*
+
+---
+
+## Installation
+
+Export functionality requires additional dependencies:
+
+```bash
+# For ONNX export (CPU inference)
+pip install sleap-nn[export]
+
+# For ONNX with GPU inference
+pip install sleap-nn[export-gpu]
+
+# For TensorRT export (NVIDIA GPUs only)
+pip install sleap-nn[tensorrt]
+```
+
+Or install all export dependencies:
+
+```bash
+pip install sleap-nn[export-gpu,tensorrt]
+```
+
+---
+
+## Quick Start
+
+### Export a Model
+
+```bash
+# Export to ONNX only
+sleap-nn export /path/to/model -o exports/my_model --format onnx
+
+# Export to TensorRT FP16 (includes ONNX)
+sleap-nn export /path/to/model -o exports/my_model --format both
+
+# Export top-down model (centroid + instance)
+sleap-nn export /path/to/centroid_model /path/to/instance_model \
+    -o exports/topdown --format both
+```
+
+### Run Inference
+
+```bash
+# Run inference on exported model
+sleap-nn predict exports/my_model video.mp4 -o predictions.slp
+
+# Use TensorRT for maximum speed
+sleap-nn predict exports/my_model video.mp4 -o predictions.slp --runtime tensorrt
+
+# Specify batch size
+sleap-nn predict exports/my_model video.mp4 -o predictions.slp --batch-size 8
+```
+
+---
+
+## `sleap-nn export`
+
+Export trained models to ONNX and/or TensorRT format.
+
+```bash
+sleap-nn export MODEL_PATH [MODEL_PATH_2] [options]
+```
+
+### Arguments
+
+| Argument | Description |
+|----------|-------------|
+| `MODEL_PATH` | Path to trained model checkpoint directory |
+| `MODEL_PATH_2` | Second model path for top-down (centroid + instance) |
+
+### Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--output-dir` | `-o` | Output directory for exported models | Required |
+| `--format` | `-f` | Export format: `onnx`, `tensorrt`, or `both` | `onnx` |
+| `--precision` | | TensorRT precision: `fp32` or `fp16` | `fp16` |
+| `--max-instances` | `-n` | Maximum instances per frame | `20` |
+| `--max-batch-size` | `-b` | Maximum batch size for dynamic shapes | `8` |
+| `--input-scale` | | Input resolution scale factor | `1.0` |
+| `--device` | | Device for export: `cuda` or `cpu` | `cuda` |
+| `--opset-version` | | ONNX opset version | `17` |
+
+### Examples
+
+**Single Instance Model**
+
+```bash
+sleap-nn export models/single_instance.n=1000 \
+    -o exports/fly_single \
+    --format both
+```
+
+**Top-Down Model (Combined)**
+
+For top-down inference, export both centroid and instance models together:
+
+```bash
+sleap-nn export models/centroid.n=1000 models/centered_instance.n=1000 \
+    -o exports/fly_topdown \
+    --format both \
+    --max-instances 20
+```
+
+**Bottom-Up Model**
+
+```bash
+sleap-nn export models/bottomup.n=2000 \
+    -o exports/mouse_bottomup \
+    --format both \
+    --max-instances 10
+```
+
+**Multiclass Models**
+
+Export models with supervised identity (class) labels:
+
+```bash
+# Bottom-up multiclass
+sleap-nn export models/multi_class_bottomup.n=1000 \
+    -o exports/flies_multiclass \
+    --format onnx
+
+# Top-down multiclass (centroid + multiclass instance)
+sleap-nn export models/centroid.n=1000 models/multi_class_topdown.n=1000 \
+    -o exports/flies_multiclass_topdown \
+    --format both
+```
+
+### Output Files
+
+After export, the output directory contains:
+
+```
+exports/my_model/
+├── model.onnx              # ONNX model
+├── model.onnx.metadata.json  # Model metadata
+├── model.trt               # TensorRT engine (if --format both/tensorrt)
+└── model.trt.metadata.json   # TensorRT metadata
+```
+
+---
+
+## `sleap-nn predict`
+
+Run inference on exported models.
+
+```bash
+sleap-nn predict EXPORT_DIR INPUT_PATH [options]
+```
+
+### Arguments
+
+| Argument | Description |
+|----------|-------------|
+| `EXPORT_DIR` | Path to exported model directory |
+| `INPUT_PATH` | Path to video file (`.mp4`, `.avi`, etc.) |
+
+### Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--output` | `-o` | Output path for predictions (`.slp`) | `<input>.predictions.slp` |
+| `--runtime` | `-r` | Runtime: `auto`, `onnx`, or `tensorrt` | `auto` |
+| `--batch-size` | `-b` | Inference batch size | `4` |
+| `--n-frames` | `-n` | Number of frames to process (0 = all) | `0` |
+| `--device` | | Device: `auto`, `cuda`, or `cpu` | `auto` |
+
+### Examples
+
+**Basic Inference**
+
+```bash
+sleap-nn predict exports/my_model video.mp4 -o predictions.slp
+```
+
+**High-Throughput TensorRT**
+
+```bash
+sleap-nn predict exports/my_model video.mp4 \
+    -o predictions.slp \
+    --runtime tensorrt \
+    --batch-size 8
+```
+
+**Process Specific Frames**
+
+```bash
+sleap-nn predict exports/my_model video.mp4 \
+    -o predictions.slp \
+    --n-frames 1000
+```
+
+**CPU Inference**
+
+```bash
+sleap-nn predict exports/my_model video.mp4 \
+    -o predictions.slp \
+    --runtime onnx \
+    --device cpu
+```
+
+---
+
+## Supported Model Types
+
+| Model Type | CLI Name | Description |
+|------------|----------|-------------|
+| Single Instance | `single_instance` | One animal per frame |
+| Centroid | `centroid` | Centroid detection only |
+| Centered Instance | `centered_instance` | Instance on cropped images |
+| Top-Down | `topdown` | Centroid + instance (combined) |
+| Bottom-Up | `bottomup` | Multi-instance with PAF grouping |
+| Multiclass Bottom-Up | `multi_class_bottomup` | Bottom-up with identity classes |
+| Multiclass Top-Down | `multi_class_topdown` | Top-down with identity classes |
+
+---
+
+## Python API
+
+### Export Models Programmatically
+
+```python
+from sleap_nn.export import export_to_onnx, export_to_tensorrt
+from sleap_nn.export.wrappers import SingleInstanceONNXWrapper
+from sleap_nn.export.metadata import build_base_metadata
+
+# Load your trained model
+model = ...  # Your trained PyTorch model
+
+# Create wrapper
+wrapper = SingleInstanceONNXWrapper(
+    backbone=model.backbone,
+    head=model.head,
+    max_instances=1,
+)
+
+# Export to ONNX
+export_to_onnx(
+    wrapper,
+    output_path="model.onnx",
+    input_shape=(1, 1, 192, 192),  # (B, C, H, W)
+    input_dtype="uint8",
+)
+
+# Export to TensorRT
+export_to_tensorrt(
+    wrapper,
+    output_path="model.trt",
+    input_shape=(1, 1, 192, 192),
+    precision="fp16",
+)
+```
+
+### Run Inference with Predictors
+
+```python
+from sleap_nn.export.predictors import ONNXPredictor, TensorRTPredictor
+import numpy as np
+
+# Load ONNX model
+predictor = ONNXPredictor("model.onnx")
+
+# Prepare input (uint8 images)
+frames = np.random.randint(0, 256, (4, 1, 192, 192), dtype=np.uint8)
+
+# Run inference
+outputs = predictor.predict(frames)
+peaks = outputs["peaks"]  # (B, N_nodes, 2)
+peak_vals = outputs["peak_vals"]  # (B, N_nodes)
+```
+
+### Load Exported Model Metadata
+
+```python
+from sleap_nn.export.metadata import load_metadata
+
+metadata = load_metadata("exports/my_model")
+print(f"Model type: {metadata.model_type}")
+print(f"Nodes: {metadata.node_names}")
+print(f"Skeleton edges: {metadata.edge_inds}")
+```
+
+---
+
+## Technical Details
+
+### Input Format
+
+Exported models expect **uint8** images in NCHW format:
+- Shape: `(batch, channels, height, width)`
+- Dtype: `uint8` (0-255)
+- Channels: 1 (grayscale) or 3 (RGB)
+
+The wrapper automatically normalizes to `[0, 1]` float32 internally.
+
+### Output Format
+
+All models output fixed-size tensors for ONNX compatibility:
+
+| Output | Shape | Description |
+|--------|-------|-------------|
+| `peaks` | `(B, N, 2)` | Keypoint coordinates (x, y) |
+| `peak_vals` | `(B, N)` | Confidence scores |
+| `peak_mask` | `(B, N)` | Valid peak mask (for variable counts) |
+
+For bottom-up models, additional outputs enable instance grouping:
+- `line_scores`: PAF scores for peak pairs
+- `candidate_mask`: Valid candidate mask
+
+### TensorRT Precision
+
+- **FP32**: Full precision, highest accuracy
+- **FP16**: Half precision, ~2x faster, minimal accuracy loss
+
+FP16 is recommended for production use on modern NVIDIA GPUs (Volta+).
+
+### Dynamic Shapes
+
+Exported models support dynamic batch sizes up to `--max-batch-size`. Height and width are fixed at export time based on the training configuration.
+
+---
+
+## Troubleshooting
+
+### ONNX Runtime CUDA Not Available
+
+If ONNX falls back to CPU:
+
+```bash
+# Check available providers
+python -c "import onnxruntime as ort; print(ort.get_available_providers())"
+```
+
+Install GPU support:
+```bash
+pip install onnxruntime-gpu
+```
+
+### TensorRT Export Fails
+
+Ensure TensorRT is properly installed:
+
+```bash
+python -c "import tensorrt as trt; print(trt.__version__)"
+```
+
+Common issues:
+- CUDA version mismatch with TensorRT
+- Insufficient GPU memory for engine building
+- Missing cuDNN libraries
+
+### Slow Bottom-Up Inference
+
+Bottom-up models require CPU-side Hungarian matching for instance grouping. This is expected and cannot be accelerated with GPU export. For maximum throughput, use larger batch sizes.
+
+### Model Metadata Missing
+
+If metadata files are missing, the model can still be loaded but node names and skeleton information won't be available. Re-export the model to generate metadata.
+
+---
+
+## Known Limitations
+
+!!! info "Current Limitations"
+    - **Standalone centroid/centered_instance prediction**: The `sleap-nn predict` command only supports combined models (top-down, bottom-up, single-instance). Standalone centroid or centered-instance models must be used via the Python API.
+    - **Bottom-up instance grouping**: PAF-based grouping runs on CPU and may be slower than GPU inference for models with many keypoints.
+    - **TensorRT engine portability**: TensorRT engines are GPU-specific and must be regenerated when moving to different GPU hardware.
+    - **Dynamic image sizes**: Height and width are fixed at export time. To support different resolutions, re-export with the desired input shape.
+
+---
+
+## See Also
+
+- [Training Guide](training.md) - Train models before export
+- [Inference Guide](inference.md) - PyTorch inference with `sleap-nn track`
+- [CLI Reference](cli.md) - Complete CLI documentation

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/docs/index.md

@@ -111,6 +111,7 @@ To run inference:
 - **[Configuration Guide](config.md)** - Detailed explanation of all configuration parameters and how to set up your config file for training
 - **[Training Guide](training.md)** - How to train models using the CLI or Python API and advanced training options
 - **[Inference Guide](inference.md)** - How to run inference and tracking with CLI/ APIs and evaluate the models
+- **[Export Guide](export.md)** - Export models to ONNX/TensorRT for high-performance inference
 - **[CLI Reference](cli.md)** - Quick reference for all command-line options
 
 #### **Tutorials**
@@ -157,4 +158,5 @@ Have questions about usage, feature requests, or want to share your experience?
 - [Configuration Guide](config.md)
 - [Training Models](training.md)
 - [Running Inference / Tracking](inference.md)
+- [Model Export](export.md)
 - [API Reference](api/index.md)

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/docs/inference.md

@@ -126,6 +126,45 @@ sleap-nn track \
 |-----------|-------------|---------|
 | `--queue_maxsize` | Maximum size of the frame buffer queue | `8` |
 
+#### Filtering Overlapping Instances
+
+SLEAP-NN can filter out duplicate/overlapping predictions after inference using greedy non-maximum suppression (NMS). This is useful for removing redundant detections without enabling full tracking.
+
+| Parameter | Description | Default |
+|-----------|-------------|---------|
+| `--filter_overlapping` | Enable filtering of overlapping instances after inference | `False` |
+| `--filter_overlapping_method` | Similarity metric: `iou` (bounding box) or `oks` (keypoint-based) | `iou` |
+| `--filter_overlapping_threshold` | Similarity threshold above which instances are considered duplicates | `0.8` |
+
+**Methods:**
+
+- **`iou`**: Uses bounding box intersection-over-union. Fast and position-based.
+- **`oks`**: Uses Object Keypoint Similarity. Pose-aware, considers keypoint distances.
+
+**Example usage:**
+
+```bash
+# Enable filtering with default IOU method
+sleap-nn track -i video.mp4 -m model/ --filter_overlapping
+
+# Use OKS method with custom threshold
+sleap-nn track -i video.mp4 -m model/ \
+    --filter_overlapping \
+    --filter_overlapping_method oks \
+    --filter_overlapping_threshold 0.5
+```
+
+**Threshold guidelines:**
+
+| Value | Effect |
+|-------|--------|
+| 0.3 | Aggressive - removes instances with >30% similarity |
+| 0.5 | Moderate - balanced filtering |
+| 0.8 | Permissive (default) - only removes highly similar instances |
+
+!!! note "Filtering vs Tracking"
+    This filtering is independent of tracking and runs before the tracking step. You can use both together—filtering removes duplicates first, then tracking assigns IDs to remaining instances.
+
 
 ## Run inference with API
 

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/mkdocs.yml

@@ -109,6 +109,7 @@ nav:
     - Configuration Setup: config.md
     - Training: training.md
     - Inference & Tracking: inference.md
+    - Exporting: export.md
     - CLI Reference: cli.md
   - Tutorials:
     - Example Notebooks: example_notebooks.md
@@ -119,4 +120,4 @@ nav:
     - Model Architectures: models.md
     - Full API: api/
   - Changelog: changelog.md
-  - Releases: https://github.com/talmolab/sleap-nn/releases
+  - Releases: https://github.com/talmolab/sleap-nn/releases

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/pyproject.toml

@@ -48,6 +48,7 @@ dependencies = [
     "jupyter",
     "jupyterlab",
     "pyzmq",
+    "rich-click>=1.9.5",
 ]
 dynamic = ["version", "readme"]
 
@@ -64,6 +65,9 @@ torch-cpu = ["torch", "torchvision>=0.20.0"]
 torch-cuda118 = ["torch", "torchvision>=0.20.0"]
 torch-cuda128 = ["torch", "torchvision>=0.20.0"]
 torch-cuda130 = ["torch", "torchvision>=0.20.0"]
+export = ["onnx>=1.15.0", "onnxruntime>=1.16.0", "onnxscript>=0.1.0"]
+export-gpu = ["onnx>=1.15.0", "onnxruntime-gpu>=1.16.0", "onnxscript>=0.1.0"]
+tensorrt = ["tensorrt>=10.0.0", "torch-tensorrt>=2.0.0"]
 
 [dependency-groups]
 # PEP 735: Dev-only dependencies (`dev` is installed automatically by `uv sync`)

{sleap_nn-0.1.0a2 → sleap_nn-0.1.0a4}/sleap_nn/__init__.py

@@ -50,7 +50,7 @@ logger.add(
     colorize=False,
 )
 
-__version__ = "0.1.0a2"
+__version__ = "0.1.0a4"
 
 # Public API
 from sleap_nn.evaluation import load_metrics