Metadata-Version: 2.4
Name: napari-sam3-assistant
Version: 0.0.1
Summary: A napari plugin for SAM3 text, box, exemplar, refinement, and 3D/video-like segmentation workflows.
Author: Wulin Teo
License: MIT
Keywords: napari,SAM3,segmentation,tracking,microscopy,image analysis
Classifier: Framework :: napari
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: napari>=0.5.0
Requires-Dist: qtpy
Requires-Dist: numpy
Requires-Dist: pillow
Dynamic: license-file

# napari-sam3-assistant

`napari-sam3-assistant` is a napari widget for running Meta SAM 3 segmentation workflows from napari image, points, shapes, labels, and text inputs.

The plugin focuses on task-based segmentation workflows:

- 2D segmentation with text, box, point, and mask-style prompts
- 3D stack / video-like propagation from prompts on a selected slice or frame
- exemplar segmentation from Shapes ROI boxes
- text-based concept segmentation
- refinement with positive and negative point prompts

SAM 3 is not bundled with this plugin. Install the SAM 3 backend and download the SAM 3 model files separately from Meta's Hugging Face repository.

## Status

This project is under active development. The current widget supports local SAM 3 model loading, napari prompt collection, background execution, and writing results back to napari layers.

## Requirements

- Python `>=3.12`
- napari `>=0.5`
- SAM 3 Python package importable as `sam3`
- PyTorch and torchvision installed for your platform
- A local SAM 3 checkpoint directory containing:
  - `config.json`
  - `processor_config.json`
  - one weight file such as `sam3.pt` or `model.safetensors`
GPU use requires a PyTorch / torchvision / SAM 3 stack that is compatible with your GPU architecture. If CUDA kernels are not available for the device, select **CPU** in the widget.

## Setup

Setup has three parts:

1. Install the SAM 3 backend.
2. Download the SAM 3 model files from Hugging Face and configure the model path.
3. Install this napari plugin.

### 1. Install SAM 3

Create and activate an environment:

```bash
conda create -n napari-sam3 python=3.12
conda activate napari-sam3
```

Install PyTorch and torchvision for your platform. Use the official PyTorch selector for the current command:

```bash
pip install torch torchvision
```

Install SAM 3:

```bash
git clone https://github.com/facebookresearch/sam3.git
cd sam3
pip install -e .
```

### 2. Download SAM 3 Weights

This plugin does not ship with SAM 3 weights or model configuration files. Download them from the official Hugging Face repository:

```text
https://huggingface.co/facebook/sam3
```

The repository is gated.

1. Sign in to your Hugging Face account.
2. Open the facebook/sam3 model page.
3. Request or accept access to the repository.
4. Once access is approved, open the Files and versions tab.
5. Download the required model and configuration files directly from the website.

A reference screenshot of the file list is shown below:

![SAM 3 model files screenshot](docs/sam3_model_files.png)


Expected model directory:

```text
~/models/sam3/
  config.json
  processor_config.json
  sam3.pt
```

`model.safetensors` is also supported as a weight file. Depending on the Hugging Face layout, the directory may also contain tokenizer files such as `tokenizer.json`, `vocab.json`, and `merges.txt`.

Keep all downloaded model files together in one directory. In the plugin widget, click `Browse`, select that directory, then click `Validate`.

For this project, a local folder such as the following is acceptable:

```text
~/Projects/napari/sam3/model
```
Note that the upstream SAM 3 source repository does not ship with a model/ folder by default. In this project, sam3/model is a user-created local directory used to store downloaded SAM 3 weights and configuration files.

If you created sam3/model yourself and placed the downloaded Hugging Face files there, that is a valid setup. The important requirement is simply that all required SAM 3 files stay together in one readable directory and that you select that directory in the widget.

The selected model directory is remembered by the widget.

### 3. Install napari-sam3-assistant

Install this plugin:

```bash
git clone https://github.com/wulinteousa2-hash/napari-sam3-assistant
cd napari-sam3-assistant
pip install -e .
```

Start napari:

```bash
napari
```

Open the widget from:

```text
Plugins > SAM3 Assistant
```

## Basic Workflow

1. Open an image in napari.
2. Open `Plugins > SAM3 Assistant`.
3. Select the image in `Napari Layers > Image`.
4. Select a task.
5. Create a prompt layer if the task needs one.
6. Click `Run Preview`.
7. Inspect `SAM3 preview labels`, `SAM3 preview masks`, or `SAM3 preview boxes`.
8. Click `Save Result as Labels` to keep the result.

Use `Clear Preview` to remove generated preview layers without deleting prompts or saved labels.

## Tasks

### Text Segmentation

Use text to segment all matching instances of a concept.

Workflow:

1. Set `Task` to `Text segmentation`.
2. Leave `Prompt tool` as `Text only`.
3. Enter a short phrase, for example:

```text
cell
nucleus
myelin
myelin sheath
```

4. Click `Run Preview`.

No prompt layer is needed for text segmentation. `Create Prompt Layer` is not required.

Text prompts usually work better as short noun phrases than instructions. Prefer `myelin sheath` over `segment all the myelin rings`.

If the result says `objects=0`, SAM 3 ran but did not return masks above threshold.

### 2D Segmentation With Boxes

Use boxes to identify the target object or concept.

Workflow:

1. Set `Task` to `2D segmentation`.
2. Set `Prompt tool` to `Box`.
3. Click `Create Prompt Layer`.
4. Draw one or more rectangles in the `SAM3 boxes` Shapes layer.
5. Click `Run Preview`.

The output appears in preview layers.

### Exemplar Segmentation

Use example ROIs to segment similar objects.

Workflow:

1. Set `Task` to `Exemplar segmentation`.
2. Set `Prompt tool` to `Box`.
3. Click `Create Prompt Layer`.
4. Draw boxes around one or more example objects.
5. Click `Run Preview`.

The local SAM 3 image API exposes visual exemplars through geometric box prompts. The plugin stores ROI metadata, but inference currently passes exemplar ROIs as SAM 3 visual box prompts.

### Refinement With Positive and Negative Points

Use points to correct a result.

Workflow:

1. Set `Task` to `Refinement`.
2. Set `Prompt tool` to `Points (+/-)`.
3. Click `Create Prompt Layer`.
4. Choose `Positive` and add points on regions to include.
5. Choose `Negative` and add points on regions to exclude.
6. Click `Run Preview`.

This is useful after a text, box, or exemplar preview is close but not correct.

### Labels Mask Prompt

Use a napari Labels layer as a mask-style prompt.

Workflow:

1. Set a task that supports mask prompts.
2. Set `Prompt tool` to `Labels mask`.
3. Click `Create Prompt Layer`.
4. Paint non-zero pixels in `SAM3 mask prompt`.
5. Click `Run Preview`.

### 3D Stack / Video Propagation

Treat a stack as video-like data and propagate a prompt through frames or slices.

Workflow:

1. Open a stack in napari.
2. Set `Task` to `3D/video propagation`.
3. Select the target frame or slice in napari.
4. Create a prompt layer and add prompts on that frame.
5. Choose propagation direction:
   - `both`
   - `forward`
   - `backward`
6. Click `Run Preview` or `Propagate Stack/Video`.

Preview output is written to:

```text
SAM3 propagated preview labels
```

Saved output is written to:

```text
SAM3 saved propagated labels
```

The current SAM 3 video predictor backend is CUDA-only. CPU mode is supported for 2D/image workflows, not 3D/video propagation.

## Channel Axis

`Channel axis` tells the plugin which data axis is color/channel.

Default:

```text
-1
```

Use `-1` for grayscale images and normal RGB/RGBA images. The plugin auto-detects trailing RGB/RGBA axes of size `3` or `4`.

Examples:

```text
(H, W)          -> -1
(H, W, 3)      -> -1
(H, W, 4)      -> -1
(Z, H, W)      -> -1
(C, H, W)      -> 0
(Z, C, H, W)   -> 1
(T, C, H, W)   -> 1
(Z, H, W, C)   -> 3
```

Leave it at `-1` unless your image has an explicit multi-channel microscopy dimension.

## Output Layers

Preview layers:

```text
SAM3 preview labels
SAM3 preview masks
SAM3 preview boxes
SAM3 propagated preview labels
```

Saved layers:

```text
SAM3 saved labels
SAM3 saved propagated labels
```

Buttons:

- `Validate`: check the selected SAM 3 model directory.
- `Load Image Model`: load the 2D/image model.
- `Load 3D/Video Model`: load the video propagation model.
- `Run Preview`: run the selected task.
- `Clear Preview`: remove generated preview layers only.
- `Save Result as Labels`: copy preview labels into saved labels.
- `Cancel`: stop a running worker.
- `Unload`: unload the SAM3 model from memory.

## ARM64, CUDA, and DGX Spark

For ARM64 systems such as NVIDIA DGX Spark / GB10:

- Use Python 3.12 or newer.
- Keep the NVIDIA driver and CUDA stack current.
- Install a PyTorch/torchvision build that supports your GPU architecture.
- Use `CPU` mode for reliable 2D execution if CUDA kernels are unavailable.
- Use explicit `CUDA` only when testing a compatible GPU build.

Check PyTorch GPU support:

```bash
python - <<'PY'
import torch
print("torch:", torch.__version__)
print("torch cuda runtime:", torch.version.cuda)
print("cuda available:", torch.cuda.is_available())
if torch.cuda.is_available():
    print("device:", torch.cuda.get_device_name(0))
    print("capability:", torch.cuda.get_device_capability(0))
    print("arch list:", torch.cuda.get_arch_list())
PY
```

GB10 reports compute capability `12.1` (`sm_121`). If your PyTorch build does not include compatible kernels, you may see:

```text
CUDA error: no kernel image is available for execution on the device
nvrtc: error: invalid value for --gpu-architecture
```

The plugin does not compile PyTorch, torchvision, or SAM 3 CUDA extensions.

## Troubleshooting

### No mask appears and status says `objects=0`

SAM 3 returned no detections above threshold. Try:

- a shorter text prompt
- a more common concept phrase
- box or exemplar prompts
- CPU mode if the CUDA path is unstable

### CUDA kernel image error

Error:

```text
CUDA error: no kernel image is available for execution on the device
```

The GPU is visible, but at least one required CUDA kernel was not built for the device architecture. Use `CPU`, or install compatible PyTorch/torchvision/SAM 3 builds.

### Invalid GPU architecture

Error:

```text
nvrtc: error: invalid value for --gpu-architecture
```

The installed PyTorch CUDA runtime cannot compile for the detected GPU. Use `CPU` or install a build that supports the GPU.

### BFloat16 conversion errors

The plugin converts SAM3 `bfloat16` outputs to `float32` before writing NumPy-backed napari layers. If you still see dtype errors, restart napari after changing device mode and run again.

### Text prompt creates no layer

That is expected. Text segmentation does not need a prompt layer. Enter text and click `Run Preview`.

## Development

Install in editable mode:

```bash
pip install -e .
```

Run tests:

```bash
PYTHONPATH=src pytest -q
```

The test suite covers coordinate mapping, prompt collection, adapter utility behavior, and static widget UI checks. It does not download SAM 3 weights.

## References

- SAM 3 repository: https://github.com/facebookresearch/sam3
- SAM 3 model files: https://huggingface.co/facebook/sam3
- PyTorch installation selector: https://pytorch.org/get-started/locally/

## License

MIT. See the project license file.
