Thresholds to rotation and scaling

[simomounir]

Hi,

I ll never stop saying it, but thanks for maintaining and making valis better in every release.

I have a question regarding putting guard-rails in registration. Is there a way to tell Valis to not go beyond a range of rotation and/or scaling when performing alignment of a set of images? Maybe there is a way but could not find anything in documentation.

Thanks a lot

[cdgatenbee]

Hi @simomounir,

So glad to hear your finding valis useful! It really great to hear from people who are using it in their research. I know the updates have slowed down, but I am trying to keep up with the issues and adding improvements. Regarding your question, right now there isn't exactly a way to limit scaling or rotations, but valis does check if the proposed transformation makes things worse than not doing anything at all. This is done just by checking if the aligned features are further apart after registration than before, and if they are, the rigid transformation matrix is just set to the identity matrix (serial_rigid.check_M). But are you having issues where it seems like the scaling or rotation is excessive? It's possible that this check is getting skipped somewhere.

Best,
-Chandler

P.S. Apologies for not getting back to you on Issue 236. Were you able to figure it out?

[simomounir]

Thanks for the prompt response and for keeping this resource up and maintained.

1- Yes, trying to align two DAPI images, with quite faint signal. So maybe indeed that check is getting skipped. I can also maybe upload the images I tried to align and which one I used as reference.

So I do know as prior knowledge that scaling and rotation will never go beyond a certain range, as that can also make alignment faster when work load is heavy. Should i use a processor optimized for getting DAPI features?

2- As for #236 , I think I had to actually find the mapping used between pixels and physical unit. Before that I got results that did not make much sense. I have some tests to run this week, I can let you know if that solved it. Thanks a lot!