Structure ids from annotation atlas do not match the structure ids in the json graph (mouse brain)

Technical
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1

Hi,

I have downloaded:

  • http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_25.nrrd (adult mouse brain annotation atlas, 25µm)
  • http://api.brain-map.org/api/v2/structure_graph_download/1.json (JSON file which i think is the corresponding structure graph)

I think both are the latest version available.

However, among the 619 unique ids in the annotation atlas, 21 are not matching any in the JSON file:

{0, # universe
997,
182305696,
182305712,
312782560,
312782592,
312782656,
484682464,
526157184,
526322272,
527696992,
549009216,
560581568,
563807424,
576073728,
589508416,
589508480,
599626944,
606826624,
606826688,
607344832,
614454272,}

Some of this ids look familiar (but not identical) in the JSON, like in the isocortex:

 480149202   Rostrolateral lateral visual area   
 182305689   Primary somatosensory area, unassigned 
 480149230   Laterolateral anterior visual area 
 312782574   Laterointermediate area  
 312782628   Postrhinal area 
 480149258   Mediomedial anterior visual area 
 480149286   Mediomedial posterior visual area 
 480149314   Medial visual area 
 312782546   Anterior area

… along with their children structures

How can I find a version of the JSON that matches the CCF3_2017 annotation atlas (or a version of the atlas that matches the structure graph)?

Best,
Etienne

2

Hi @edoumazane,

I think there might be some issues in the way you are accessing/opening annotation_25.nrrd
Note that you have to read it as 64-bit unsigned int values.

This gist shows how to open the file using SimpleITK and count the number of unique values.
unique_value_counts.py (github.com)

Resulting in:
value_count.csv (github.com)

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3

Hi @lydian,
Thank you very much for your help.

I was opening the annotation atlas NRRD file with ImageJ and saving it as a TIFF file (don’t do that!).

Accessing the annotation atlas NRRD file directly with SimpleITK, as you suggested, did the trick and solved my annotation problem.

As mentioned in CCFv3 annotation: wrong IDs - #4 by NicoKiaru, ImageJ fails to handle biggest integers properly because uint32 (which range from 0 to 4 294 967 295 = 2^32 -1) are converted into float32 (not precise enough for integers above 16 777 215 = 2^24 - 1).

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