Looking at individual cores and annotate results (datasheet)

Hi. I am using TMA dearrayer and it works great. I wonder if there is a way to look at individual cores and be able to annotate them for an excel sheet later. For example, looking at ERG positive prostate cancer slides one by one, and just typing the results for later analysis.

There should be! Try this:

  • Select a core (any core)
  • Press Enter. This should show a dialog where you can enter any ‘Note’
  • Type something
  • Press Enter again to dismiss the note dialog
  • Use an arrow key to navigate to another core in the grid, then repeat

The ‘Note’ column should appear in any TMA results table.

Using this method, if your ‘Note’ is a manual score (perhaps a number 0-9) then it is possible manually score a TMA using 4 keypresses per core. But you can also write longer notes if needed.

Thanks. It works perfectly.

I have a few humble suggestions:

  1. be to be able to add more notes, for different variables. One example would be for each core I would give Gleason grade (one field), % of pattern 4 (second field) and PTEN status (third field) to be in the table.

  2. A more advanced method would also permit go over the whole TMA one by one, without the need to select the core and press enter.

  3. In the TMA dearrayer, the possibility to label the cores continuously (e.g. I have four TMAs mapped 1-70 each, making the cores 1-280).

I thought someone wrote a script that popped up each individual core and let you choose something, but going back to the old forum I wasn’t able to find it quickly.
Ah, here it is. It might be the sort of thing that could be adapted to do what you want.
https://groups.google.com/d/msg/qupath-users/HYRSCf_ctyE/Kj5chJNXBgAJ
Though, like many things, that would take some coding.

You can try this script:

i = 1
for (core in getTMACoreList()) {
    core.setName(Integer.toString(i))
    i++
}
fireHierarchyUpdate()

I will keep the other suggestions in mind for the future.

For now I’m afraid it is limited to one field in QuPath, although you could enter multiple values there using some kind of separator between them, and then split these to different columns in a spreadsheet application later.