update readme

README.md

@@ -30,19 +30,19 @@ VollSeg comes with different options to combine CARE based denoising with UNET,
 
 | Example Image | Description | Training Data | Trained Model | GT image   | Optimal combination  | Notebook Code | Model Prediction | Metrics |
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-| <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 | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Ascadian_Embryo.ipynb) |<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="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="images/Ascadian_GT.png" title="GT Ascadian Embryo" width="200"> | UNET model, slice_merge = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Ascadian_Embryo.ipynb) |<img src="images/Ascadian_pred.png" title="Prediction Ascadian Embryo" width="200" > | <img src="images/Metrics_Ascadian.png" title="Metrics Ascadian Embryo" width="200" >  |
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-| <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 | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Mamary_gland.ipynb) |<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="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="images/Carcinoma_GT.png" title="GT Carcinoma" width="200"> | StarDist model + Denoising Model, dounet = False | [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_Mamary_gland.ipynb) |<img src="images/Carcinoma_pred.png" title="Prediction Carcinoma Cells" width="200" > | <img src="images/Metrics_carcinoma.png" title="Metrics Carcinoma Cells" width="200" >  |
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-| <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| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_tissue_segmentation.ipynb) |<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  |
+| <img src="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="images/Xenopus_tissue_GT.png" title="GT Xenopus Tissue" width="200"> | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_tissue_segmentation.ipynb) |<img src="images/Xenopus_tissue_pred.png" title="Prediction Xenopus Tissue" width="200" > | No Metrics  |
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-| <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/microtubule_kymo_raw.png"  title="Raw Microtubule Kymograph" width="200">| TIRF + MultiKymograph Fiji tool 2D single channel| [Training Dataset](https://zenodo.org/record/6355705/files/Microtubule_edgedetector_training.zip)| [UNET Model](https://zenodo.org/record/6355705/)  |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/microtubule_kymo_GT.png" title="GT Microtubule Kymograph" width="200"> | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/microtubule_kymo_pred.png" title="Prediction Microtubule Kymographe" width="200" > | No Metrics  |
+| <img src="images/microtubule_kymo_raw.png"  title="Raw Microtubule Kymograph" width="200">| TIRF + MultiKymograph Fiji tool 2D single channel| [Training Dataset](https://zenodo.org/record/6355705/files/Microtubule_edgedetector_training.zip)| [UNET Model](https://zenodo.org/record/6355705/)  |<img src="images/microtubule_kymo_GT.png" title="GT Microtubule Kymograph" width="200"> | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) |<img src="images/microtubule_kymo_pred.png" title="Prediction Microtubule Kymographe" width="200" > | No Metrics  |
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-| <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/lung_xray_raw.png"  title="Raw Lung Xray" width="200">| XRay of Lung 2D single channel| [Training Dataset](https://www.kaggle.com/nikhilpandey360/lung-segmentation-from-chest-x-ray-dataset)| [UNET Model](https://zenodo.org/record/6060177/)  |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/lung_xray_GT.png" title="GT Lung Xray" width="200"> | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/lung_xray_pred.png" title="Prediction Lung Xray" width="200" > | <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Metrics_lung_xray.png" title="Metrics Lung Xray" width="200" >   |
+| <img src="images/lung_xray_raw.png"  title="Raw Lung Xray" width="200">| XRay of Lung 2D single channel| [Training Dataset](https://www.kaggle.com/nikhilpandey360/lung-segmentation-from-chest-x-ray-dataset)| [UNET Model](https://zenodo.org/record/6060177/)  |<img src="images/lung_xray_GT.png" title="GT Lung Xray" width="200"> | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) |<img src="images/lung_xray_pred.png" title="Prediction Lung Xray" width="200" > | <img src="images/Metrics_lung_xray.png" title="Metrics Lung Xray" width="200" >   |
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-| <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/nuclei_mask_raw.png"  title="Raw Nuclei Mask" width="200">| LaserScanningConfocalMicroscopy 2D single channell| [Test Dataset](https://zenodo.org/record/6359349/)|Private |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/nuclei_mask_GT.png" title="GT Nuclei Mask" width="200"> | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/nuclei_mask_pred.png" title="Prediction Nuclei Mask" width="200" > | No metrics   |
+| <img src="images/nuclei_mask_raw.png"  title="Raw Nuclei Mask" width="200">| LaserScanningConfocalMicroscopy 2D single channell| [Test Dataset](https://zenodo.org/record/6359349/)|Private |<img src="images/nuclei_mask_GT.png" title="GT Nuclei Mask" width="200"> | UNET model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_Microtubule_kymo_segmentation.ipynb) |<img src="images/nuclei_mask_pred.png" title="Prediction Nuclei Mask" width="200" > | No metrics   |
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-| <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/nuclei_raw.png"  title="Raw Nuclei" width="200">| LaserScanningConfocalMicroscopy 3D single channell| [Test Dataset](https://zenodo.org/record/6359295/)|Private |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/nuclei_GT.png" title="GT Nuclei" width="200"> | UNET model + StarDist model + ROI model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_star_roi.ipynb) |<img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/nuclei_pred.png" title="Prediction Nuclei" width="200" > |  <img src="https://github.com/kapoorlab/vollseg-napari/blob/main/vollseg_napari/images/Metrics_nuclei.png" title="Metrics Nuclei" width="200" >   |
+| <img src="images/nuclei_raw.png"  title="Raw Nuclei" width="200">| LaserScanningConfocalMicroscopy 3D single channell| [Test Dataset](https://zenodo.org/record/6359295/)|Private |<img src="images/nuclei_GT.png" title="GT Nuclei" width="200"> | UNET model + StarDist model + ROI model| [Colab Notebook](https://github.com/kapoorlab/VollSeg/blob/main/examples/Predict/Colab_VollSeg_star_roi.ipynb) |<img src="images/nuclei_pred.png" title="Prediction Nuclei" width="200" > |  <img src="images/Metrics_nuclei.png" title="Metrics Nuclei" width="200" >   |
 
 
 ## Troubleshooting & Support