I would like to cut a ROI of my hippocampus’ slice in order to count my cells just in the CA1 area.
In order to do so, I select “object classification workflow” > “choose export image settings” - when we select our x start, the program doesn’t compute it as a start point at all and doesn’t cut our image on the x-axis from my selected starting point.
What I am doing wrong?
good to see you here.
now, for the roi export. I tried it out with the following settings:
please note, that the output image description also reflects the cutout shape.
Now having said that, do you happen to have an image mask of the region you are interested in? (that would be an image with 1s wherever you want to count something and 0s wherever you are not interested in). With that you can count in arbitrary regions by adding it as an
Atlas image in the input data applet/tab.
Are you using the two workflows separately, btw?
Coming to think of it a bit more, if your goal is counting, why not filter the objects in the exported table by x-coordinate?