Merge branch 'main' into maisi

Author: Can-Zhao

README.md

@@ -226,6 +226,12 @@ This tutorial shows how to train a surgical tool segmentation model to locate to
 ##### [endoscopic inbody classification](./computer_assisted_intervention/endoscopic_inbody_classification.ipynb)
 Tutorial to show the pipeline of fine tuning an endoscopic inbody classification model based on a corresponding pretrained bundle.
 
+#### <ins>**Hugging Face**</ins>
+##### [MONAI Hugging Face Pipeline](./hugging_face/hugging_face_pipeline_for_monai.ipynb)
+This tutorial demonstrates how to encapsulate an existing MONAI model workflow into a Hugging Face pipeline, which is widely adopted by the open-source community.
+##### [Fine-tuning for Hugging Face Pipeline](./hugging_face/finetune_vista3d_for_hugging_face_pipeline.ipynb)
+This tutorial explains the process of fine-tuning a VISTA3D model and integrating it into a Hugging Face pipeline for inference.
+
 #### <ins>**Modules**</ins>
 ##### [bundle](./bundle)
 Get started tutorial and concrete training / inference examples for MONAI bundle features.

figures/hugging_face_general.jpg

@@ -57,6 +57,7 @@
    "outputs": [],
    "source": [
     "!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel]\"\n",
+    "!python -c \"import skimage\" || pip install -q scikit-image\n",
     "!python -c \"import vtk\" || pip install -q vtk\n",
     "!python -c \"import pxr\" || pip install -q usd-core\n",
     "!python -c \"import trimesh\" || pip install -q trimesh\n",
@@ -466,6 +467,11 @@
     "    print(f\"Saved whole segmentation {all_organ_filename}\")\n",
     "\n",
     "\n",
+    "# if workflow.run() is uncommented and run, an image and a label files will be generated in the output folder\n",
+    "# for example, file paths are like this:\n",
+    "# f\"{bundle_root}/output/sample_20250317_065034_415537_image.nii.gz\"\n",
+    "# f\"{bundle_root}/output/sample_20250317_065034_415537_label.nii.gz\"\n",
+    "# then you can replace the \"input_nii_path\" below with the generated label file\n",
     "input_nii_path = f\"{bundle_root}/datasets/IntegrationTest-AbdomenCT.nii.gz\"\n",
     "output_nii_path = f\"{bundle_root}/datasets/monai/nii\"\n",
     "output_obj_path = f\"{bundle_root}/datasets/monai/obj\"\n",

figures/hugging_face_model.jpg

@@ -82,6 +82,7 @@ doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" mask_augmentation_e
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" maisi_inference_tutorial.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" realism_diversity_metrics.ipynb)
 doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" omniverse_integration.ipynb)
+doesnt_contain_max_epochs=("${doesnt_contain_max_epochs[@]}" hugging_face_pipeline_for_monai.ipynb)
 
 # Execution of the notebook in these folders / with the filename cannot be automated
 skip_run_papermill=()
@@ -129,6 +130,7 @@ skip_run_papermill=("${skip_run_papermill[@]}" .*nuclick_infer.ipynb*)  # https:
 skip_run_papermill=("${skip_run_papermill[@]}" .*unet_segmentation_3d_ignite_clearml.ipynb*)  # https://github.com/Project-MONAI/tutorials/issues/1555
 skip_run_papermill=("${skip_run_papermill[@]}" .*vista_2d_tutorial_monai.ipynb*)
 skip_run_papermill=("${skip_run_papermill[@]}" .*learn2reg_oasis_unpaired_brain_mr.ipynb*)
+skip_run_papermill=("${skip_run_papermill[@]}" .*finetune_vista3d_for_hugging_face_pipeline.ipynb*)
 
 # output formatting
 separator=""