enh: add notebook demonstrating access to data from Imaging Data Commons

README.md

@@ -331,6 +331,8 @@ Illustrate reading NIfTI files and iterating over image patches of the volumes l
 This tutorial illustrates the flexible network APIs and utilities.
 ##### [postprocessing_transforms](./modules/postprocessing_transforms.ipynb)
 This notebook shows the usage of several postprocessing transforms based on the model output of spleen segmentation task.
+##### [idc_dataset](./modules/idc_dataset.ipynb)
+This notebook shows how to query and download public cancer imaging data from NCI Imaging Data Commons (IDC) using `idc-index`, and how to load DICOM images and DICOM-SEG segmentations into MONAI for AI/ML preprocessing.
 ##### [public_datasets](./modules/public_datasets.ipynb)
 This notebook shows how to quickly set up training workflow based on `MedNISTDataset` and `DecathlonDataset`, and how to create a new dataset.
 ##### [tcia_csv_processing](./modules/tcia_csv_processing.ipynb)
@@ -386,4 +388,3 @@ Example shows the use cases of using MONAI to evaluate the performance of a gene
 
 #### [VISTA2D](./vista_2d)
 This tutorial demonstrates how to train a cell segmentation model using the [MONAI](https://monai.io/) framework and the [Segment Anything Model (SAM)](https://github.com/facebookresearch/segment-anything) on the [Cellpose dataset](https://www.cellpose.org/).
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runner.sh

@@ -50,6 +50,7 @@ doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" 2d_slices_from_3d_t
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" preprocess_to_build_detection_dataset.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" preprocess_detect_scene_and_split_fold.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" preprocess_extract_images_from_video.ipynb)
+doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" idc_dataset.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" profiling_camelyon_pipeline.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" monailabel_HelloWorld_radiology_3dslicer.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" monailabel_monaibundle_3dslicer_multiorgan_seg.ipynb)
@@ -97,6 +98,7 @@ skip_run_papermill=("${skip_run_papermill[@]}" .*generate_random_permutations*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*transforms_update_meta_data*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*video_seg*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*tcia_dataset*)
+skip_run_papermill=("${skip_run_papermill[@]}" .*idc_dataset*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*hovernet_torch*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*preprocess_detect_scene_and_split_fold*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*preprocess_to_build_detection_dataset*)