diff --git a/README.md b/README.md index f1af10192..6e6f7c88a 100644 --- a/README.md +++ b/README.md @@ -157,7 +157,7 @@ This folder provides a simple baseline method for training, validation, and infe This notebook demonstrates how to construct a training workflow of UNETR on multi-organ segmentation task using the BTCV challenge dataset. ##### [unetr_btcv_segmentation_3d_lightning](./3d_segmentation/unetr_btcv_segmentation_3d_lightning.ipynb) This tutorial demonstrates how MONAI can be used in conjunction with [PyTorch Lightning](https://www.pytorchlightning.ai/) framework to construct a training workflow of UNETR on multi-organ segmentation task using the BTCV challenge dataset. -##### [vista3d](./3d_segmentation/vista3d) +##### [vista3d](./vista_3d) This tutorial showcases the process of fine-tuning VISTA3D on [MSD Spleen dataset](http://medicaldecathlon.com) using MONAI. For an in-depth exploration, please visit the [VISTA](https://github.com/Project-MONAI/VISTA) repository. #### **2D registration** diff --git a/deepedit/ignite/README.md b/deepedit/ignite/README.md index 3d7f76672..16a97bf35 100644 --- a/deepedit/ignite/README.md +++ b/deepedit/ignite/README.md @@ -92,7 +92,7 @@ python ./train.py --export true ``` -#### [DeepEdit Inference](./inference.ipynb) +#### [DeepEdit Inference](./infoANDinference.ipynb) This notebook helps to run any pre-transforms before running inference over a DeepEdit single label model. It also helps to run post-transforms to get the final label mask. diff --git a/generation/README.md b/generation/README.md index 6c4fe96aa..34b492c4a 100644 --- a/generation/README.md +++ b/generation/README.md @@ -74,10 +74,10 @@ Example shows the use cases of applying a spatial VAE to a 2D synthesis example. Example shows the use cases of applying a spatial VAE to a 3D synthesis example. To obtain realistic results, the model is trained on the original VAE losses, as well as perceptual and adversarial ones. ## Performing anomaly detection with diffusion models: [implicit guidance](./anomaly_detection/2d_classifierfree_guidance_anomalydetection_tutorial.ipynb), [using transformers](./anomaly_detection/anomaly_detection_with_transformers.ipynb) and [classifier free guidance](./anomaly_detection/anomalydetection_tutorial_classifier_guidance.ipynb) -Examples show how to perform anomaly detection in 2D, using implicit guidance [2D-classifier free guiance](./anomaly_detection/2d_classifierfree_guidance_anomalydetection_tutorial.ipynb), transformers [using transformers](./anomaly_detection/anomaly_detection_with_transformers.ipynb) and [classifier free guidance](./anomalydetection_tutorial_classifier_guidance). +Examples show how to perform anomaly detection in 2D, using implicit guidance [2D-classifier free guiance](./anomaly_detection/2d_classifierfree_guidance_anomalydetection_tutorial.ipynb), transformers [using transformers](./anomaly_detection/anomaly_detection_with_transformers.ipynb) and [classifier free guidance](./anomaly_detection/anomalydetection_tutorial_classifier_guidance.ipynb). ## 2D super-resolution using diffusion models: [using torch](./2d_super_resolution/2d_sd_super_resolution.ipynb) and [using torch lightning](./2d_super_resolution/2d_sd_super_resolution_lightning.ipynb). Examples show how to perform super-resolution in 2D, using PyTorch and PyTorch Lightning. -## [Guiding the synthetic process using a semantic encoder](./2d_diffusion_autoencoder/2d_diffusion_autoencoder.ipynb) +## [Guiding the synthetic process using a semantic encoder](./2d_diffusion_autoencoder/2d_diffusion_autoencoder_tutorial.ipynb) Example shows how to train a DDPM and an encoder simultaneously, resulting in the latents of the encoder guiding the inference process of the DDPM. diff --git a/monailabel/README.md b/monailabel/README.md index 3a06ba2a5..ecd33d6f8 100644 --- a/monailabel/README.md +++ b/monailabel/README.md @@ -24,7 +24,7 @@ Each tutorial provides MONAI Label plugin installation steps associated with the - [MONAILabel: Pancreas Tumor Segmentation with 3D Slicer](monailabel_bring_your_own_data.ipynb): Pancreas and tumor segmentation with CT scans in 3D Slicer. - [MONAILabel: Multi-organ Segmentation with 3D Slicer](monailabel_monaibundle_3dslicer_multiorgan_seg.ipynb): Multi-organ segmentation with CT scans in 3D Slicer. - [MONAILabel: Whole Body CT Segmentation with 3D Slicer](monailabel_wholebody_totalSegmentator_3dslicer.ipynb): Whole body (104 structures) segmentation with CT scans. - - [MONAILabel: Lung nodule CT Detection with 3D Slicer](monaibundle_3dslicer_lung_nodule_detection.ipynb): Lung nodule detection task with CT scans. + - [MONAILabel: Lung nodule CT Detection with 3D Slicer](monailabel_monaibundle_3dslicer_lung_nodule_detection.ipynb): Lung nodule detection task with CT scans. - **Pathology App**: - Viewer: [QuPath](https://qupath.github.io/) | Datastore: Local | Task: Segmentation - [MONAILabel: Nuclei Segmentation with QuPath](monailabel_pathology_nuclei_segmentation_QuPath.ipynb) Nuclei segmentation with QuPath setup and Nuclick models.