Dear all,
I have a quick question regarding the shifting centre using volume alignment tool. There are a few problem I am facing, but I will go one by one.
So, the first thing first, am I doing it correctly? These are the results of re-centering before and after. Here, I have defined the new coords as 79, 79, 26. Reasonable?
- I have linked both the refined map and the particles to input
- I have ticked the box “Reassign UIDs” to the particle processing parameter
- The only warning I received as I didn’t specified the unit of the coords, so it considered as pixels (voxels).
I am raising this as on the next step I tried to extract with a smaller box (256 px) around the new centre (made sure that the “Recenter using aligned shift” box was ticked), but during the 2D, it turns out it didn’t extract from the area of interest adequately. For example, there were around ~4000 ptcls, but I ended up with only a few hundreds.
N.B. I have tried with a mask as well, but that I will discuss that separately. Another future discussion would be, this ptcls are probably wrongly aligned, as you could see my feature of interest on both sides - and that’s how they were in the 2D as well, which is not suppose to happen.