Cell instances should contain big brain coordinates as well
x_um y_um area_um2
cell_id
1 -3.622802 -12.077647 25.524589
... ... ... ...
siibra-python requires x,y,z values for digesting point clouds such as cell distiributions. It makes sense for x_um and y_um to stay but would be great to have coordinates in bigbrain space. It can have x_bigbrain_mm type of column names which I can map to x,y,z. Needs a few changes on siibra-python but not so difficult.
So given a tsv
x_um y_um area_um2 x_bigbrain_mm y_bigbrain_mm z_bigbrain_mm
cell_id
1 -3.622802 -12.077647 25.524589 1 4 5
... ... ... ... 23 2 55
The reader could look like:
pd.read_csv('./test.csv', index_col=0, skiprows=1, names=['cell id', 'x_patch_um', 'y_patch_um', 'area_um2', 'x', 'y', 'z'])
which could be in configuration json as:
"decoder": {
"@type": "siibra/decoder/csv",
"delimiter": "\\t",
"engine": "python",
"header": 0,
"index_col": 0,
"skiprows": 1
}
Edited by Ahmet Nihat Simsek