I’ve started to catalogue some of the human ISH data for a project, and as a part of that process, I’m looking through the xml files for each donor. I’m not sure whether there’s a reference or white paper out there that explains the structure of the xml file (i.e., what each column is, and what the values represent within a column). Apologies for the length, but for reference, I have included the column names here beneath this post. Across the images you’ll see repetitions of some column names, however I’ve noticed in the actual xml, despite two columns having the same name, they have different values. Perhaps that’s the same parameter for a different aspect of the data? Is there a white paper or technical reference that explains the structure of the xml? Please let me know.
Thanks again for the continued assistance!
Please see below for screenshots of column names - numbers indicate column position from left to right (generated using RStudio IDE).
Hello @MPanday, this might be helpful, In Situ Hybridization (ISH) Data - Allen Human Brain Atlas. To provide you with a more targeted answer can you provide examples of the columns/data types you are specifically looking at and specific example images to which you are referring?
Thanks for sending the link to the ISH help page! Though my question pertains specifically to understanding the XML files that I download for a specific image. I’ve included a screenshot of a specific donor and the XML file access to which I was referring previously.
Once I’m in an XML file (not necessarily this specific human donor’s XML), I’d like to get a better sense of what the different column names represent (after I open the file in MS Excel), and what information is available within the file. I’ve included the column names from an xml file in my earlier post, but I’d like to know whether there’s a technical reference that specifically explains what information is present in an XML file.
I was wondering if you were able to resolve this issue as I have the same question. I was able to view the structure as a list in R so I’ve been able to figure out character classes such as sample id and age, but I’m having trouble figuring out how the ISH quantification is called. Any help is much appreciated, thank you!
