clearmap results ID different than Allen Region ID

[etayaloni]

The index of each pixel in the ABA atlas has a corrospondant id name in allen atlas.
however, when looking at the index of the registered output files (Result.1.mhd) the index is different and do not corrospondan to the allen athlas.
Can we save the original allen ID in the output files for later proccessing? instad of the transformed ones?
For example, in the attached image of output registered athlas for a specific section, when we check the ID in the cerebalum region, it apperes coresponding to different allen area index table.
Many thanks,
Etay

[crousseau]

Hi,
You're looking at the result of the second step of the alignment, which is the reference brain aligned to your data. ClearMap then applies the inverse transformation to the coordinates of cells (in the space of your raw data) to bring them to the space of the reference brain and finally looks up at the corresponding label in the "annotation" file. It is this "annotation" file which contains the unique integer values (what we call "id") of the Allen brain atlas.
So, the value 257 that you read in the image is not related to the atlas annotation - is it the autofluorescence signal intensity?
(for the sake of completeness, in the table, 257 is the line number, also called "order" or "graph order", and the Allen's structure "id" is 516 in this case).
I hope this clarifies things a bit