more small fixes

Author: fedorov

notebooks/collections_demos/nlm_visible_human_project.ipynb

@@ -15,15 +15,15 @@
       "source": [
         "# Visible Human Project @ NCI Imaging Data Commons\n",
         "\n",
-        "National Library of Medicine **[Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) dataset (VHD)** was released in 1994. Since then, VHD enabled [a large number of studies](https://scholar.google.com/scholar?cites=14936044487090373990&as_sdt=40000005&sciodt=0,22&hl=en), including development of the [Insight Toolkit](https://itk.org/) and its initial release in 2002 (check out this 2003 [publication by Michael Ackerman and Terry Yoo](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480240/) for the historical perspective). For a long time, access to VHD required obtaining a license, but recently NLM lifted that requirement. While the access to the data was opene, [downloading it from the NLM](https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/index.html) was somewhat suboptimal, and more importantly, radiology data was shared in a [proprietary format that predated DICOM](https://discourse.slicer.org/t/visible-human-project-mri-dataset-loading/8034/4), complicating its use.\n",
+        "National Library of Medicine **[Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) dataset (VHD)** was released in 1994. Since then, VHD enabled [a large number of studies](https://scholar.google.com/scholar?cites=14936044487090373990&as_sdt=40000005&sciodt=0,22&hl=en), including development of the [Insight Toolkit](https://itk.org/) and its initial release in 2002 (check out this 2003 [publication by Michael Ackerman and Terry Yoo](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480240/) for the historical perspective). For a long time, access to VHD required obtaining a license, but recently NLM lifted that requirement. While the access to the data was opened, [downloading it from the NLM website](https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/index.html) was somewhat suboptimal, and more importantly, radiology data was shared in a [proprietary format that predated DICOM](https://discourse.slicer.org/t/visible-human-project-mri-dataset-loading/8034/4), complicating its use.\n",
         "\n",
         "In July 2023, VHD was included in the v15 data release by the [NCI Imaging Data Commons](https://portal.imaging.datacommons.cancer.gov/explore/filters/?collection_id=nlm_visible_human_project). With the release of VHD on IDC:\n",
         "* VHD images are available harmonized into standard DICOM representation\n",
         "* radiology images can be visualized directly in the browser using IDC Portal (e.g., see this [CT series](https://viewer.imaging.datacommons.cancer.gov/viewer/1.3.6.1.4.1.5962.1.2.370.1672334394.26545?SeriesInstanceUID=1.3.6.1.4.1.5962.1.3.370.2.1672334394.26545) of the Visible Female)\n",
         "* metadata accompanying VHD is searchable\n",
         "* image files are available from either Google Cloud Platform or AWS buckets, and can be downloaded efficiently at any level (e.g., as the entire collection, or individual DICOM series)\n",
         "\n",
-        "The IDC release of the VHD dataset includes both the radiology (CT and MR) and digitized cryosections images for both Visible Male and Visible Female. As part of data harmonization, images were converted into standard DICOM representation (from the original [proprietary GE Signa format](https://discourse.slicer.org/t/visible-human-project-mri-dataset-loading/8034/) and PNG for the radiology and cryosection images, respectively), while maintaining the acquisition metadata in standard DICOM fields. Cryosection images are available as External Camera Photography (XC) modality DICOM series.\n",
+        "The IDC release of the VHD dataset includes both the radiology (CT and MR) and digitized cryosections images for both Visible Male and Visible Female. As part of data harmonization, images were converted into standard DICOM representation (from the original proprietary GE Signa format and PNG for the radiology and cryosection images, respectively), while maintaining the acquisition metadata in standard DICOM fields. Cryosection images are available as External Camera Photography (XC) modality DICOM series.\n",
         "\n",
         "In this notebook we demonstrate interoperability and visualization of DICOM XC cryosection images using off-the-shelf open source tools.\n",
         "\n",
@@ -281,13 +281,14 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "0Ypgkc-n9-0d"
+        "id": "0Ypgkc-n9-0d",
+        "cellView": "form"
       },
       "outputs": [],
       "source": [
         "#@title Enter your Project ID\n",
         "# initialize this variable with your Google Cloud Project ID!\n",
-        "my_ProjectID = \"idc-sandbox-000\" #@param {type:\"string\"}\n",
+        "my_ProjectID = \"\" #@param {type:\"string\"}\n",
         "\n",
         "import os\n",
         "os.environ[\"GCP_PROJECT_ID\"] = my_ProjectID\n",
@@ -1036,7 +1037,7 @@
         "# download the file\n",
         "!./s5cmd --no-sign-request --endpoint-url https://s3.amazonaws.com cp {sample_url} .\n",
         "\n",
-        "image = load_dicom_xc_slice(\"./\"+sample_url.split(\"/\")[-1])\n",
+        "image = load_vhd_xc_slice(\"./\"+sample_url.split(\"/\")[-1])\n",
         "\n",
         "fig1 = plt.figure(figsize = (20,20))\n",
         "ax1 = fig1.add_subplot()\n",