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The reason the realignment process was not working is due to the neuroglancer URL belonging to the wrong animal.
It looks like the user created a new url from an old one and the old/wrong animal carried on through.
I fixed the database entry and will push code where the thumbnail_realigned directory will be visible.
Song-Mao wants the realigned dir put back so we can compare the 1st and 2nd alignment steps.
Sorry for the confusion. The original issue was solely about the realignment process. Actually, keeping the realigned sections in a folder named C1T_aligned (instead of using a different name C1T_realigned) could make the naming "equivalent" to the cases where realignment task was never run. Was this the reason why the usage of name C1T_realigned was deprecated previously?
The reason the realignment process was not working is due to the neuroglancer URL belonging to the wrong animal.
It looks like the user created a n
I forgot to assign the cloned Neuroglancer State to the new animal ID. In other words, before adding fiducial points, users should make sure the animal ID is assigned correctly? We will edit the tutorials about this.
We'll change the code so only C1 downsampled needs the realignment step. The C1/thumbnail_realigned will remain.
Check DK229.
Users don't need the realigned directories under C2/C3
For C1, there will only be full_aligned.
The process will now only create the realigned directory under C1 and when downsample = True. It will not create a realigned directory when downsample is False, nor when the channel is 2 or 3 or 4 ...
It will also check for fiducials when you run the realign process. If it finds none, it will give a warning and exit.
When creating the neuroglancer data, it will look for both aligned and realigned directories. It will initially search for a realigned directory and use that if it exists, otherwise it will use the aligned directory. This is to make sure that everything still works with animals that still have a realigned dir.
Activity
eddyod commentedon Sep 17, 2025
The reason the realignment process was not working is due to the neuroglancer URL belonging to the wrong animal.
It looks like the user created a new url from an old one and the old/wrong animal carried on through.
I fixed the database entry and will push code where the thumbnail_realigned directory will be visible.
eddyod commentedon Sep 17, 2025
It is now fixed. Needs to be tested at full resolution.
soliao commentedon Sep 17, 2025
Sorry for the confusion. The original issue was solely about the realignment process. Actually, keeping the realigned sections in a folder named C1T_aligned (instead of using a different name C1T_realigned) could make the naming "equivalent" to the cases where realignment task was never run. Was this the reason why the usage of name C1T_realigned was deprecated previously?
I forgot to assign the cloned Neuroglancer State to the new animal ID. In other words, before adding fiducial points, users should make sure the animal ID is assigned correctly? We will edit the tutorials about this.
Thank you!
soliao commentedon Sep 17, 2025
As the usage of C1T_realigned has been restored, I think we can stay with this. I will see if the full resolution images can align correctly.
eddyod commentedon Sep 24, 2025
We'll change the code so only C1 downsampled needs the realignment step. The C1/thumbnail_realigned will remain.
Check DK229.
Users don't need the realigned directories under C2/C3
For C1, there will only be full_aligned.
eddyod commentedon Sep 24, 2025
When a user runs the realignment process, the program should look for fiducial points and if there are none, it should warn the user.
eddyod commentedon Sep 24, 2025
The process will now only create the realigned directory under C1 and when downsample = True. It will not create a realigned directory when downsample is False, nor when the channel is 2 or 3 or 4 ...
It will also check for fiducials when you run the realign process. If it finds none, it will give a warning and exit.
When creating the neuroglancer data, it will look for both aligned and realigned directories. It will initially search for a realigned directory and use that if it exists, otherwise it will use the aligned directory. This is to make sure that everything still works with animals that still have a realigned dir.
soliao commentedon Sep 25, 2025
2025-09-25
Tested and confirmed that the realignment is automatically applied on C2 correctly at low resolution.
Will move on and test at full resolution.