| --- |
| title: DynaCell Virtual Staining Demo |
| emoji: 🔬 |
| colorFrom: gray |
| colorTo: gray |
| sdk: gradio |
| sdk_version: "5.29.0" |
| app_file: app.py |
| pinned: false |
| python_version: "3.12" |
| suggested_hardware: zero-a10g |
| models: |
| - biohub/dynacell-checkpoints |
| datasets: |
| - biohub/dynacell-demo-data |
| --- |
| |
| # DynaCell Virtual Staining Demo |
|
|
| Predict fluorescence channels (membrane, nuclei, or organelle structure) from phase-contrast OME-Zarr using three models: |
|
|
| - **CELL-Diff** — flow-matching diffusion model |
| - **FNet3D** — 3-D U-Net (FNet architecture) |
| - **VSCyto3D** — masked-autoencoder pretrained U-Net |
|
|
| ## Quick start |
|
|
| 1. Select an organelle from the dropdown. |
| 2. Click **Load Demo Data** to fetch the matching A549-cell demo dataset directly into the Space — no download/upload needed. |
| 3. Run predictions in **Tab 1** or generate the CELL-Diff ODE trajectory in **Tab 2**. |
|
|
| ## Using your own data |
|
|
| The input must be an OME-Zarr HCS store zipped into a single `.zip` file, with layout: |
|
|
| ``` |
| your_data.zarr/ |
| 0/0/fov0000/0 # array shape (T, C, Z, Y, X) |
| # C[0] = Phase3D, Z = 16, YX = 512×512 |
| ``` |
|
|
| Use [iohub](https://github.com/czbiohub-sf/iohub) to create compatible zarr stores. |
|
|
