---
license: bsd-3-clause
library_name: onnx
tags:
  - onnx
  - spot-detection
  - fluorescence-microscopy
  - bioimage-analysis
  - spotiflow
---

# Spotiflow ONNX — General

ONNX export of the **general** pretrained [Spotiflow](https://github.com/weigertlab/spotiflow) model for 2D fluorescent spot detection in microscopy images.

## Model Details

| Property | Value |
|---|---|
| Architecture | Spotiflow (U-Net backbone + stereographic flow head) |
| Input | `float32 [B, 1, H, W]` — single-channel grayscale image |
| Output 0 | `float32 [B, 1, H, W]` — heatmap (pre-sigmoid logits) |
| Output 1 | `float32 [B, 3, H, W]` — stereographic flow `(z, y, x)` |
| ONNX opset | 16 |
| Pretrained variant | `general` |

## Usage

### Python (onnxruntime)

```python
import onnxruntime as ort
import numpy as np

session = ort.InferenceSession("model.onnx")
image = np.random.rand(1, 1, 512, 512).astype(np.float32)
outputs = session.run(None, {"input": image})
heatmaps, flow = outputs[0], outputs[-1]  # flow has shape [B, 3, H, W]
```

### Rust (spotiflow-rs)

```rust
use spotiflow_rs::{SpotiflowSession, PredictParams};

let mut session = SpotiflowSession::new("model.onnx")?;
let (spots, heatmaps, flows) = session.predict(&image_f32, h, w, PredictParams::default())?;
```

## Export

Exported from the official PyTorch weights using a wrapper that converts the model's dictionary output to an explicit `(heatmaps, flow)` tuple for correct ONNX tracing:

```bash
python scripts/export_onnx.py --model general --output model.onnx
```

## License

BSD 3-Clause — same as the [original Spotiflow repository](https://github.com/weigertlab/spotiflow).

Copyright (c) 2023, Albert Dominguez Mantes, Martin Weigert.

## Citation

```bibtex
@article{dominguez2024spotiflow,
  title={Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression},
  author={Dominguez Mantes, Albert and Herrera, Antonio and Khven, Irina and Schlaeppi, Anjalie and Aho, Eftychia and Erskine, Amber and Laubscher, Eleonora and Hendriks, Gert-Jan and Thiran, Jean-Philippe and Bhatt, Deepak K and Wegner, Joerg D and Weigert, Martin},
  journal={bioRxiv},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}
```