allen_cord_20um atlas weird lookup_df

[RobertoDF]

Hi! I am trying to use the heatmap, but if I set the atlas like this it raise an error due to the acronym (TH for example) not being present in the lookout_df:

values = dict(  # scalar values for each region
    TH=1,
    RSP=0.2,
    AI=0.4,
    SS=-3,
    MO=2.6,
    PVZ=-4,
    LZ=-3,
    VIS=2,
    AUD=0.3,
    RHP=-0.2,
    STR=0.5,
    CB=0.5,
    FRP=-1.7,
    HIP=3,
    PA=-4,
)

scene = bgh.Heatmap(
    values,
    position=(8000, 5000, 5000),
    orientation="frontal",  # or 'sagittal', or 'horizontal' or a tuple (x,y,z)
    thickness=1000,
    title="frontal",
   atlas_name="allen_cord_20um"
    vmin=-5,
    vmax=3,
    format="3D",
)

The lookout_df indeed contains only "weird acronyms":

atlas = Atlas(atlas_name="allen_cord_20um")
atlas.lookup_df:
acronym id  name
1Sp 1   Lamina 1
2Ssp    2   Lamina 2 Outer part
2Spl    3   Lamina 2 Inner part
3Sp 4   Lamina 3
4Sp 5   Lamina 4
IB  6   Internal basilar nucleus_4Sp
5Sp 7   Lamina 5
5SpL    8   Lamina 5 Lateral part
5SpM    9   Lamina 5 Medial part
D   10  Dorsal nucleus (Clarke)_5Sp

• OS: Linux brainglobe-atlasapi 2.0.6 pypi_0 pypi brainglobe-heatmap 0.5.3 pypi_0 pypi brainglobe-space 1.0.2 pypi_0 pypi brainglobe-utils 0.5.0 pypi_0 pypi brainrender 2.1.9 pypi_0 pypi

[alessandrofelder]

(Not an expert neuroanatomist) are those acronyms not what is expected for the allen spinal cord atlas @RobertoDF? Are you wanting to use a spinal cord or a brain atlas?

[RobertoDF]

oh! my mistake , didnt notice cord. I read it as coord. Closing now. Thanks!