diff --git a/open_access/image_data_commons.md b/open_access/image_data_commons.md deleted file mode 100644 index c8f67a10..00000000 --- a/open_access/image_data_commons.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -order: 996 ---- - -# Accessing Images via Image Data Commons (IDC) - -HTAN Imaging Level 2 data is now available through the [NCI Imaging Data Commons (IDC)](https://portal.imaging.datacommons.cancer.gov/). - -Imaging Data Commons hosts versions of the HTAN Imaging Level 2 data converted to [DICOM-TIFF dual personality files](https://learn.canceridc.dev/dicom/dicom-tiff-dual-personality-files). For further information and an example open source implementation, see [online reference](https://www.sciencedirect.com/science/article/pii/S2153353922003753#!). - -For further information on using the IDC, you can explore their [online documentation](https://learn.canceridc.dev/). - -## Filtering for HTAN Images in the IDC portal - -From the [homepage of the Imaging Data Commons](https://portal.imaging.datacommons.cancer.gov/), click the purple **Explore** link to explore image data. - -HTAN data can be selected by selecting in the **Collection** group in the left-hand bar (you may need to click "show more" to reveal all collections). - -![IDC: Filter for HTAN Images](../img/idc1.png) - -Pie charts show the breakdown of selected metadata attributes. - -By checking collections (e.g. HTAN WUSTL), cases (participants), studies (biospecimens), and series (images), the study instances of selected images may be found. - -![IDC: Filter for HTAN Images](../img/idc2.png) - -## Download Images from IDC - -HTAN data is shared under a CC-BY 4.0 license, and is available to download as DICOM images without egress costs from IDC thanks to support from the Google public datasets program. For complete details, see [IDC Documentation on Downloading Data](https://learn.canceridc.dev/data/downloading-data). Basic download instructions are also included on the HTAN portal for files released by the IDC, by selecting the filename. - -![HTAN Data Portal: IDC Download Details](../img/idc3.png) - -Note that individual DICOM files representing each channel and pyramid level may need to be sorted or converted back to TIFF files for reuse in image analysis tools. - -## Viewing Images via the IDC SLIM Viewer - -Clicking they **eye icon** in the view column on the IDC portal, or the **IDC** link when hovering over the thumbnail in the HTAN portal, takes the user to IDC’s interactive SLIM viewer. This interactive viewer provides image exploration and pre-rendered scenes. - -![IDC: Interactive SLIM Viewer](../img/idc4.png)