Hi, I am currently looking to see if there is any way to export the image data in the table that is nested under the 'values and control' window. That is, the transformation, x, y, and z coordinates. We would like to use this data for our project, however recording numerous values for 30+ images per hemisphere is not quite feasible.
Thanks for any help!
Hi,
Those coordinates are the midpoints of the given images, so they also incorporate deviations coming from where/how the tissue sample is located/oriented on the slide. Unfortunately it's not easy to see where they point to: when you launch QuickNII, but don't load an image series, hovering the mouse over the values and control box makes a crosshair appear, that's where the coordinates come from.
Anyway, assuming that part is okay for your use case, yes, it's straightforward to create a utility that produces those coordinates. Would you mind naming the atlas in question, and if you have a preferred set of the transformations (some atlases have many of them)?
Best regards,
Gergely Csucs
Hello, we are using QuickNII with the rat atlas WHSRat-v4.
We use image series for mapping recording these values for each image in the series compared across multiple brains may prove useful to be able to compare deviations.
Ideally, we would like to be able to take down all of the transformations in this atlas that is:
voxels, WHS (mm), bregma (mm), lambda (mm), WHS (voxels), bregma (voxels).
Best regards,
Cooper Payne
Hi,
https://www.nesys.uio.no/QuickNII/coordinates.html may be doing what you ask for. It allows you to select a QuickNII series descriptor (JSON format is supported only), and then it immediately attempts to "download" an Excel file containing the coordinates in question. Because of this aspect the file will likely appear in the downloads folder of the browser.
I hope this helps, best regards,
Gergely
Hi,
I will double check with my team, but that appears to be exactly what we were looking for! Brilliant!
Thank you so much for the assistance!
Best regards,
Cooper Payne