Integration of annotated MNI space for human brain.

BICCN / cell-locator

manually align specimens to annotated 3D spaces

https://cell-locator.readthedocs.io

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Closed jcfr closed 4 years ago

jcfr commented 4 years ago

What's the problem this feature will solve?

In the context of the Patch-seq workflow, the Human neuroanatomy team at Allen may perform pinning for human specimen.

We are using ICBM 152 symmetric template 2009b:

Describe the solution you'd like

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jcfr commented 4 years ago

@wbwakeman

Would it be possible to provide the 3D annotations along with the ontology ?

Which data should be loaded in the application: pd, t1 or t2 ?

wbwakeman commented 4 years ago

@jcfr Thanks for opening this issue to track the work. I will see if I can track down someone that may have answers to your questions.

jcfr commented 4 years ago

Would it be possible to provide the 3D annotations along with the ontology ?

See also TERMS OF USE for proper acknowledgment

wbwakeman commented 4 years ago

Please use the T1: mni_icbm152_t1_tal_nlin_sym_09b_hires.nii

Yes, it is possible to use the Allen Human reference described in the forum link.

jcfr commented 4 years ago

Since the MNI and the CCF datasets are associated with different workflow, I am thinking about:

adding a command line argument called --atlas-type that could take the value CCF or MNI
saving the atlas type in the annotation file
adding a combox in the application allowing to switch between the two dataset

Does that make sense ?

wbwakeman commented 4 years ago

Makes sense to me

jcfr commented 4 years ago

For reference, some screenshot illustrating the MNI loaded in Slicer (note that the color mapping is not the correct one)

with annotation converted to independent segments and rendered as surface in 3D:

jcfr commented 4 years ago