This section of the documentation complements the digital pathology self-guided python notebooks tutorials available in our notebooks repository:
Getting started with pathology images in IDC: all of the pathology images in IDC are in DICOM Slide Microscopy format; this notebook will help you get started with using this representation and also searching IDC pathology images.
Exploring IDC slide microscopy images metadata: introduction to the key metadata accompanying IDC slide microscopy images that can be used for subsetting data and building cohorts.
In the following subsections you will find notebooks that don't require python programming, or have dependencies that make them not suitable for the python notebook format.
QuPath is a popular open-source desktop application for visualizing and annotating slide microscopy images. It is integrated with both OpenSlide and BioFormats libraries, and as of the current QuPath 0.5.1 version supports direct loading of DICOM Slide Microscopy images. In this tutorial you will learn how to use DICOM SM images from IDC with QuPath.
First you will need to download a sample SM image from IDC to your desktop. To identify a sample image, you can navigate to the IDC Portal, copy SeriesInstanceUID value for a sample SM series you want to download. Given that UID, you can download the corresponding files using idc-index python package (see details in the documentation section describing data download instructions).
In this tutorial, we will use the series identified by SeriesInstanceUID from the collection 1.3.6.1.4.1.5962.99.1.3140643155.174517037.1639523215699.2.0, which you can download as follows:
Next, open QuPath and select "File > Open".
Choose just one of the .dcm files that belong to the desired dataset, then click Open. The remaining files will be automatically detected and should not be selected.
When prompted for an image type, select Brightfield H&E (or whatever is appropriate for the dataset being opened), then click Apply. This is a QuPath feature intended to aid in analysis, and is further described in the .
The image should now display, and can be navigated by zooming/panning as described in the .
Zooming and panning in real time:
The Image tab on the left side of the screen shows dimension information, and lists any associated images. In this case, a thumbnail image is present under Associated Images at the bottom of the Image tab. Double-clicking on Series 1 (THUMBNAIL) will open the thumbnail image in a separate window:
For this part, we will use a slide from the HTAN-OHSU collection identified by SeriesInstanceUID 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.4.0. As before, you can download it as follows:
As in the brightfield case, open QuPath and select File > Open.
Choose just one of the .dcm files in the dataset, as the other files will be automatically detected. It does not matter which file is selected. When prompted, set the image type to Fluorescence, or as appropriate for the dataset:
The image should then display, and can be navigated by zooming/panning as described in the .
The Image tab indicates the number of channels (12 in this case). By default, all channels will be displayed at once. This can be changed by selecting View > Brightness/Contrast or the "half-circles" icon in the toolbar:
Unchecking the Show box will hide the channel's data, and update the image.
idc download 1.3.6.1.4.1.5962.99.1.3140643155.174517037.1639523215699.2.0idc download 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.4.0
