docs: update cellpose-js links to TheJacksonLaboratory/cellpose-js
Browse files
README.md
CHANGED
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@@ -24,7 +24,7 @@ language:
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Single-file FP16 ONNX export of **Cellpose-SAM** (CPSAM), the ViT-L–based cellular
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segmentation model from [Stringer et al., 2025](https://www.biorxiv.org/content/10.1101/2025.04.28.651001v1).
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Intended for in-browser inference via WebGPU through
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[`cellpose-js`](https://github.com/
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ONNX Runtime backend that supports opset 18 and FP16 graph IO.
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- **Architecture:** SAM ViT-L image encoder (modified — patch size 8, no windowed
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@@ -84,7 +84,7 @@ const result = await cp.segment(
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The first call fetches 588 MB from the Hub; subsequent calls hit IndexedDB and
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cold-start in under ~2 s.
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See the [cellpose-js README](https://github.com/
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for the full API, parameter reference, and Python parity notes.
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### With ONNX Runtime directly (Python)
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@@ -101,7 +101,7 @@ flow_y, flow_x, cellprob = out[0, 0], out[0, 1], out[0, 2]
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For flow-dynamics postprocessing (Euler integration → convergence clustering →
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connected components → size/flow filtering), use either:
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- the JS port in [`cellpose-js/src/dynamics`](https://github.com/
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- the original Python implementation in
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[`cellpose.dynamics`](https://cellpose.readthedocs.io/) — input/output
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contracts match.
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@@ -139,8 +139,8 @@ ORT-web 1.26 is ~2.3× faster than 1.20 on the WebGPU kernels — the steady-sta
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## How the model was generated
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The export path is documented in
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[`docs/STAGE0-RESULTS.md`](https://github.com/
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and [`docs/PLAN.md §1.5, §2`](https://github.com/
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The short version:
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1. **Source weights**: `mouseland/cellpose-sam` (PyTorch, 1.23 GB, 304.6 M params).
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@@ -243,7 +243,7 @@ https://www.biorxiv.org/content/10.1101/2025.04.28.651001v1
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- **Source checkpoint:** `mouseland/cellpose-sam` on Hugging Face Hub.
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- **Export scripts and ONNX artifact ETag** (`52fd6881…`) are recorded in
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[`docs/STAGE0-RESULTS.md`](https://github.com/
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- **Parity test fixtures** (numpy-generated FP32 reference tiles + expected
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flow outputs) live in `tests/fixtures/` in the `cellpose-js` repo.
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@@ -263,7 +263,7 @@ https://www.biorxiv.org/content/10.1101/2025.04.28.651001v1
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## Related
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- **Code:** [`
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- **npm:** [`cellpose-js`](https://www.npmjs.com/package/cellpose-js).
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- **Upstream:** [`MouseLand/cellpose`](https://github.com/MouseLand/cellpose) and [`mouseland/cellpose-sam`](https://huggingface.co/mouseland/cellpose-sam).
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- **Paper:** [Cellpose-SAM (bioRxiv 2025.04.28)](https://www.biorxiv.org/content/10.1101/2025.04.28.651001v1).
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Single-file FP16 ONNX export of **Cellpose-SAM** (CPSAM), the ViT-L–based cellular
|
| 25 |
segmentation model from [Stringer et al., 2025](https://www.biorxiv.org/content/10.1101/2025.04.28.651001v1).
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Intended for in-browser inference via WebGPU through
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+
[`cellpose-js`](https://github.com/TheJacksonLaboratory/cellpose-js), but usable from any
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ONNX Runtime backend that supports opset 18 and FP16 graph IO.
|
| 29 |
|
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- **Architecture:** SAM ViT-L image encoder (modified — patch size 8, no windowed
|
|
|
|
| 84 |
The first call fetches 588 MB from the Hub; subsequent calls hit IndexedDB and
|
| 85 |
cold-start in under ~2 s.
|
| 86 |
|
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+
See the [cellpose-js README](https://github.com/TheJacksonLaboratory/cellpose-js#readme)
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for the full API, parameter reference, and Python parity notes.
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| 89 |
|
| 90 |
### With ONNX Runtime directly (Python)
|
|
|
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| 101 |
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For flow-dynamics postprocessing (Euler integration → convergence clustering →
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| 103 |
connected components → size/flow filtering), use either:
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| 104 |
+
- the JS port in [`cellpose-js/src/dynamics`](https://github.com/TheJacksonLaboratory/cellpose-js/tree/main/src), or
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- the original Python implementation in
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[`cellpose.dynamics`](https://cellpose.readthedocs.io/) — input/output
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contracts match.
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## How the model was generated
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| 140 |
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The export path is documented in
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| 142 |
+
[`docs/STAGE0-RESULTS.md`](https://github.com/TheJacksonLaboratory/cellpose-js/blob/main/docs/STAGE0-RESULTS.md)
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and [`docs/PLAN.md §1.5, §2`](https://github.com/TheJacksonLaboratory/cellpose-js/blob/main/docs/PLAN.md).
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The short version:
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1. **Source weights**: `mouseland/cellpose-sam` (PyTorch, 1.23 GB, 304.6 M params).
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- **Source checkpoint:** `mouseland/cellpose-sam` on Hugging Face Hub.
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| 245 |
- **Export scripts and ONNX artifact ETag** (`52fd6881…`) are recorded in
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| 246 |
+
[`docs/STAGE0-RESULTS.md`](https://github.com/TheJacksonLaboratory/cellpose-js/blob/main/docs/STAGE0-RESULTS.md).
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- **Parity test fixtures** (numpy-generated FP32 reference tiles + expected
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flow outputs) live in `tests/fixtures/` in the `cellpose-js` repo.
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## Related
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- **Code:** [`TheJacksonLaboratory/cellpose-js`](https://github.com/TheJacksonLaboratory/cellpose-js) — TypeScript inference + dynamics port.
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- **npm:** [`cellpose-js`](https://www.npmjs.com/package/cellpose-js).
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- **Upstream:** [`MouseLand/cellpose`](https://github.com/MouseLand/cellpose) and [`mouseland/cellpose-sam`](https://huggingface.co/mouseland/cellpose-sam).
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- **Paper:** [Cellpose-SAM (bioRxiv 2025.04.28)](https://www.biorxiv.org/content/10.1101/2025.04.28.651001v1).
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