ABC project is a great work for the field.Recently i’m trying to integrate mouse ABC with MRI through CCF coordinates.MRI image has been registered to 100um CCF template and I notice ABC CCF Coordinates have also been released ,which is a huge progress i think.
But during integration, I found in the same section of ABC,such as one coronal section, the section is separated into several parts along AP axis due to CCF registeration.I wonder how the registeration was been down and how can i adjust these separated parts in resonable way.
transferatiom from CCF Coordinates by ABC to voxel Coordinates by 100um template is easy,for example, one cell has (9.423592,3.769583,2.810703) in 10um space then it will have (94,38,28) in 100um voxel space.
here is one coronal section,it is separated into several parts along AP axis.
these separated parts can be set in the same AP Coordinates to form the whole section(left);MRI FA in CCF(right)
Thanks for your interest in our resource. I believe the discrepancies you are seeing are caused by the fact that when we section brains for MERSCOPE experiments we can never perfectly recapitulate the sectioning angle in the CCF, but instead there are some yaw and tilt introduced. Because of this we generally transfer to CCF labels to section than the other way around when look at individual sections.
Sincerest apologies for the off-topic message, however I have a question for you regarding the use of the R package wholebrain. I see you made a post on the wholebrain gitter room 2 years ago, where you found that certain bregma co-ordinate parameters (I.e. between (-1.655)-(-1.955), resulted in failure of the registration command to construct an atlas. Did you ever find an anwser to this problem? I am encountering it in my own analysis, and is causing me a huge headache.
