I am working with the glioblastoma data and finding it difficult to associate the SubIDs with particular images, which from my understanding is needed to download the images. Where can I find the SubID for a specific image on the specimen page? Or, is there a “donor name” with the glioblastoma data that can be used with the previously posted image download code to mass search for these IDs?
Thank you so much for your time.
Sub image ID is available in the URL for an image. For example, the experiment here shows imageID=265851306 in a screenshot below (boxed in red), which can then be used in an image download URL command like so:
There is also a post from another issue here, that describes image downloading for the Glioblastoma dataset more generally.
Images can also be accessed for download from viewers associated with the Experiment or parent Specimen pages. When you click the download image box directly from an image display window, you will see a imageseries ID in the file name: 265851304_1.jpg means imageseries ID 265851304 (image #1 is a jpg file to download), in this example from Specimen 264632322. The second image in this series (in this case, the H&E data) would be 266291528_2.jpg and is accessible from the adjacent Download Image box.
Thank you for your help! How do you download the H&E view of the image?
The same approach can be taken to download an H&E image, as described in the previous post. From the Specimen page, select the H&E view from the Image Display dropdown menu option (the screenshot above defaults to TumorFeatureBoundary view); then click on the download image box in the upper-right corner of the H&E image display window, and you will be prompted to download an image.
Is there a way to specify this in the initial request (such as in the view=tumor_feature_annotation)? I have noticed that the SubIDs are the same for these two images, and these SubIDs also don’t seem to work with the Image Download API. Thank you again.
Sorry for the confusion - we have lots of different IDs here! Unfortunately the imageseries IDs are not the same as (or interchangeable with) the Sub image IDs. The API provides a list of class terms and associations/hierarchies which might be useful.
For this particular atlas and project, the only way to find the Sub image ID is in the URL as Wayne described above - and this is what you need for use with the API. The other examples are for downloading images directly from the image display webpage, without using the API.