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kapoorlab committed Sep 4, 2023
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11 changes: 6 additions & 5 deletions README.md
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Expand Up @@ -27,11 +27,12 @@ If you use this plugin for your research, please [cite us](http://conference.sci
## Examples

VollSeg comes with different options to combine CARE based denoising with UNET, StarDist and segmentation in a region of interest (ROI). We present some examples which are represent optimal combination of these different modes for segmenting different cell types. We summarize this in the table below:
| Example Image | Description | Training Data | Trained Model | GT image | Optimal combination | Model Prediction | Metrics |
| --- | --- |--- | --- |--- | --- |--- | --- |
| ![Raw Ascadian Embryo](images/Ascadian_raw.png)| Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) |![GT Ascadian Embryo](images/Ascadian_GT.png) | UNET model, slice_merge = False |![Prediction Ascadian Embryo](images/Ascadian_pred.png) | ![Metrics Ascadian](images/Metrics_Ascadian.png)|
| ![Raw Carcinoma](images/Carcinoma_raw.png)| Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) |![GT Carcinoma](images/Carcinoma_GT.png) | StarDist model + Denoising Model, dounet = False |![Prediction Carcinoma Cells](images/Carcinoma_pred.png) | ![Metrics Carcinoma Cells](images/Metrics_carcinoma.png) |
| ![Raw Xenopus Tissue](images/Xenopus_tissue_raw.png)| LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) |![GT Xenopus Tissue](images/Xenopus_tissue_GT.png) | UNET model|![Prediction Xenopus Tissue](images/Xenopus_tissue_pred.png) | No Metrics |
| Example Image | Description | Training Data | Trained Model |
| --- | --- |--- | --- |
| ![Raw Ascadian Embryo](images/Ascadian_raw.png)| Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) |
| ![Raw Carcinoma](images/Carcinoma_raw.png)| Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) |
| ![Raw Xenopus Tissue](images/Xenopus_tissue_raw.png)| LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) |



## Troubleshooting & Support
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49 changes: 11 additions & 38 deletions _build/html/README.html
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Expand Up @@ -399,60 +399,33 @@ <h2>Examples<a class="headerlink" href="#examples" title="Permalink to this head
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Ascadian_raw.png" title="Raw Ascadian Embryo" width="200"></p></td>
<tr class="row-even"><td><p><img alt="Raw Ascadian Embryo" src="_images/Ascadian_raw.png" /></p></td>
<td><p>Light sheet fused from four angles 3D single channel</p></td>
<td><p><a class="reference external" href="https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5">Training Data ~320 GB</a></p></td>
<td><p><a class="reference external" href="https://zenodo.org/record/6337699">UNET model</a></p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Ascadian_GT.png" title="GT Ascadian Embryo" width="200"></p></td>
<td><p><img alt="GT Ascadian Embryo" src="_images/Ascadian_GT.png" /></p></td>
<td><p>UNET model, slice_merge = False</p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Ascadian_pred.png" title="Prediction Ascadian Embryo" width="200" ></p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Metrics_Ascadian.png" title="Metrics Ascadian Embryo" width="200" ></p></td>
<td><p><img alt="Prediction Ascadian Embryo" src="_images/Ascadian_pred.png" /></p></td>
<td><p><img alt="Metrics Ascadian" src="_images/Metrics_Ascadian.png" /></p></td>
</tr>
<tr class="row-odd"><td><p></p></td>
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</tr>
<tr class="row-even"><td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Carcinoma_raw.png" title="Raw Carcinoma" width="200"></p></td>
<tr class="row-odd"><td><p><img alt="Raw Carcinoma" src="_images/Carcinoma_raw.png" /></p></td>
<td><p>Confocal microscopy 3D single channel 8 bit</p></td>
<td><p><a class="reference external" href="https://zenodo.org/record/5904082#.Yi8-BnrMJD8">Training Data</a></p></td>
<td><p><a class="reference external" href="https://zenodo.org/record/5910645/">Denoising Model</a> and <a class="reference external" href="https://zenodo.org/record/6354077/">StarDist Model</a></p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Carcinoma_GT.png" title="GT Carcinoma" width="200"></p></td>
<td><p><img alt="GT Carcinoma" src="_images/Carcinoma_GT.png" /></p></td>
<td><p>StarDist model + Denoising Model, dounet = False</p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Carcinoma_pred.png" title="Prediction Carcinoma Cells" width="200" ></p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Metrics_carcinoma.png" title="Metrics Carcinoma Cells" width="200" ></p></td>
</tr>
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<td><p><img alt="Prediction Carcinoma Cells" src="_images/Carcinoma_pred.png" /></p></td>
<td><p><img alt="Metrics Carcinoma Cells" src="_images/Metrics_carcinoma.png" /></p></td>
</tr>
<tr class="row-even"><td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Xenopus_tissue_raw.png" title="Raw Xenopus Tissue" width="200"></p></td>
<tr class="row-even"><td><p><img alt="Raw Xenopus Tissue" src="_images/Xenopus_tissue_raw.png" /></p></td>
<td><p>LaserScanningConfocalMicroscopy 2D single channel</p></td>
<td><p><a class="reference external" href="https://zenodo.org/record/6076614#.YjBaNnrMJD8">Dataset</a></p></td>
<td><p><a class="reference external" href="https://zenodo.org/record/6060378/">UNET Model</a></p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Xenopus_tissue_GT.png" title="GT Xenopus Tissue" width="200"></p></td>
<td><p><img alt="GT Xenopus Tissue" src="_images/Xenopus_tissue_GT.png" /></p></td>
<td><p>UNET model</p></td>
<td><p><img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Xenopus_tissue_pred.png" title="Prediction Xenopus Tissue" width="200" ></p></td>
<td><p><img alt="Prediction Xenopus Tissue" src="_images/Xenopus_tissue_pred.png" /></p></td>
<td><p>No Metrics</p></td>
</tr>
<tr class="row-odd"><td><p></p></td>
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</tr>
</tbody>
</table>
</section>
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10 changes: 3 additions & 7 deletions _build/html/_sources/README.md
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Expand Up @@ -27,15 +27,11 @@ If you use this plugin for your research, please [cite us](http://conference.sci
## Examples

VollSeg comes with different options to combine CARE based denoising with UNET, StarDist and segmentation in a region of interest (ROI). We present some examples which are represent optimal combination of these different modes for segmenting different cell types. We summarize this in the table below:

| Example Image | Description | Training Data | Trained Model | GT image | Optimal combination | Model Prediction | Metrics |
| --- | --- |--- | --- |--- | --- |--- | --- |
| <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Ascadian_raw.png" title="Raw Ascadian Embryo" width="200">| Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Ascadian_GT.png" title="GT Ascadian Embryo" width="200"> | UNET model, slice_merge = False |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Ascadian_pred.png" title="Prediction Ascadian Embryo" width="200" > | <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Metrics_Ascadian.png" title="Metrics Ascadian Embryo" width="200" > |
| | | | | | | | |
| <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Carcinoma_raw.png" title="Raw Carcinoma" width="200">| Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Carcinoma_GT.png" title="GT Carcinoma" width="200"> | StarDist model + Denoising Model, dounet = False |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Carcinoma_pred.png" title="Prediction Carcinoma Cells" width="200" > | <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Metrics_carcinoma.png" title="Metrics Carcinoma Cells" width="200" > |
| | | | | | | | |
| <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Xenopus_tissue_raw.png" title="Raw Xenopus Tissue" width="200">| LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Xenopus_tissue_GT.png" title="GT Xenopus Tissue" width="200"> | UNET model|<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Xenopus_tissue_pred.png" title="Prediction Xenopus Tissue" width="200" > | No Metrics |
| | | | | | | | |
| ![Raw Ascadian Embryo](images/Ascadian_raw.png)| Light sheet fused from four angles 3D single channel| [Training Data ~320 GB](https://figshare.com/articles/dataset/Astec-half-Pm1_Cut_at_2-cell_stage_half_Phallusia_mammillata_embryo_live_SPIM_imaging_stages_6-16_/11309570?backTo=/s/765d4361d1b073beedd5)| [UNET model](https://zenodo.org/record/6337699) |![GT Ascadian Embryo](images/Ascadian_GT.png) | UNET model, slice_merge = False |![Prediction Ascadian Embryo](images/Ascadian_pred.png) | ![Metrics Ascadian](images/Metrics_Ascadian.png)|
| ![Raw Carcinoma](images/Carcinoma_raw.png)| Confocal microscopy 3D single channel 8 bit| [Training Data](https://zenodo.org/record/5904082#.Yi8-BnrMJD8)| [Denoising Model](https://zenodo.org/record/5910645/) and [StarDist Model](https://zenodo.org/record/6354077/) |![GT Carcinoma](images/Carcinoma_GT.png) | StarDist model + Denoising Model, dounet = False |![Prediction Carcinoma Cells](images/Carcinoma_pred.png) | ![Metrics Carcinoma Cells](images/Metrics_carcinoma.png) |
| ![Raw Xenopus Tissue](images/Xenopus_tissue_raw.png)| LaserScanningConfocalMicroscopy 2D single channel| [Dataset](https://zenodo.org/record/6076614#.YjBaNnrMJD8)| [UNET Model](https://zenodo.org/record/6060378/) |![GT Xenopus Tissue](images/Xenopus_tissue_GT.png) | UNET model|![Prediction Xenopus Tissue](images/Xenopus_tissue_pred.png) | No Metrics |


## Troubleshooting & Support
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