Concatenate from dictionary

[revalescente]

Hello, I have 24 samples with the same elements and names. I'm trying to concatenate them but seems like it doesn't work. It stop at the first sample but I don't get why. I read the data as a dict {sample_name : sdata}.

spe_dict = sd.concatenate(spe_blocks, concatenate_tables = True, region_key = "region", instance_key = "cell_id")

>>> spe_blocks[samples[0]]['nuclei_counts'].obs
                     region       slide     cell_id  ...    extent  major_axis_length  minor_axis_length
aaaaaaaa-1  filtered_nuclei  full_image  aaaaaaaa-1  ...  0.734336          22.390856          16.715088
aaaaaaab-1  filtered_nuclei  full_image  aaaaaaab-1  ...  0.665591          35.952982          22.190399
aaaaaaac-1  filtered_nuclei  full_image  aaaaaaac-1  ...  0.773288          34.647159          25.419906
aaaaaaad-1  filtered_nuclei  full_image  aaaaaaad-1  ...  0.737557          27.155658          15.655043
aaaaaaaf-1  filtered_nuclei  full_image  aaaaaaaf-1  ...  0.554286          27.588200           9.553221
...                     ...         ...         ...  ...       ...                ...                ...
aaaakaaf-1  filtered_nuclei  full_image  aaaakaaf-1  ...  0.572727          23.858483          10.606041
aaaakaah-1  filtered_nuclei  full_image  aaaakaah-1  ...  0.577640          29.105765          18.097145
aaaakaai-1  filtered_nuclei  full_image  aaaakaai-1  ...  0.620915          17.394626           7.040765
aaaakaaj-1  filtered_nuclei  full_image  aaaakaaj-1  ...  0.448889          17.789848           8.546664
aaaakaak-1  filtered_nuclei  full_image  aaaakaak-1  ...  0.501832          19.694033          10.515163

[31755 rows x 9 columns]
>>> spe_blocks[samples[0]]['nuclei_counts'].uns
{'sopa_attrs': {'intensities': True, 'transcripts': True}, 'spatialdata_attrs': {'instance_key': 'cell_id', 'region': 'filtered_nuclei', 'region_key': 'region'}}

>>> spe_blocks[samples[0]]
SpatialData object
├── Images
│     ├── 'full_image': DataTree[cyx] (3, 8000, 16166), (3, 4000, 8083), (3, 2000, 4041), (3, 1000, 2020), (3, 500, 1010)
│     └── 'raster_nuclei': DataArray[cyx] (1, 7661, 13624)
├── Shapes
│     ├── 'filtered_bins': GeoDataFrame shape: (384309, 4) (2D shapes)
│     └── 'filtered_nuclei': GeoDataFrame shape: (31755, 1) (2D shapes)
└── Tables
      └── 'nuclei_counts': AnnData (31755, 32285)
with coordinate systems:
    ▸ 'blocco1', with elements:
        full_image (Images), raster_nuclei (Images), filtered_bins (Shapes), filtered_nuclei (Shapes)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/mnt/europa/valerio/.conda/envs/deepl-segment-bio/lib/python3.11/site-packages/spatialdata/_core/concatenate.py", line 139, in concatenate
    sdatas = _fix_ensure_unique_element_names(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/europa/valerio/.conda/envs/deepl-segment-bio/lib/python3.11/site-packages/spatialdata/_core/concatenate.py", line 257, in _fix_ensure_unique_element_names
    sdata = SpatialData.init_from_elements(elements, tables=tables)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/europa/valerio/.conda/envs/deepl-segment-bio/lib/python3.11/site-packages/spatialdata/_core/spatialdata.py", line 2298, in init_from_elements
    return cls(**elements_dict, attrs=attrs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/europa/valerio/.conda/envs/deepl-segment-bio/lib/python3.11/site-packages/spatialdata/_utils.py", line 270, in wrapper
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/mnt/europa/valerio/.conda/envs/deepl-segment-bio/lib/python3.11/site-packages/spatialdata/_core/spatialdata.py"
, line 156, in __init__
    with raise_validation_errors(
  File "/mnt/europa/valerio/.conda/envs/deepl-segment-bio/lib/python3.11/site-packages/spatialdata/_core/validation.py", line 382, in __exit__
    raise ValidationError(title=self._message, errors=self._collector.errors)
spatialdata._core.validation.ValidationError: Cannot construct SpatialData object, input contains invalid elements.
For renaming, please see the discussion here https://github.com/scverse/spatialdata/discussions/707 .
  tables/nuclei_counts: value.index does not match parent’s obs names:
Index are different

Index values are different (100.0 %)
[left]:  Index(['aaaaaaaa-1', 'aaaaaaab-1', 'aaaaaaac-1', 'aaaaaaad-1', 'aaaaaaaf-1',
       'aaaaaaag-1', 'aaaaaaam-1', 'aaaaaaap-1', 'aaaaaabb-1', 'aaaaaabd-1',
       ...
       'aaaajppo-1', 'aaaajppp-1', 'aaaakaaa-1', 'aaaakaab-1', 'aaaakaad-1',
       'aaaakaaf-1', 'aaaakaah-1', 'aaaakaai-1', 'aaaakaaj-1', 'aaaakaak-1'],
      dtype='object', length=31755)
[right]: Index(['aaaaaaaa-1-blocco1_c26STAT3', 'aaaaaaab-1-blocco1_c26STAT3',
       'aaaaaaac-1-blocco1_c26STAT3', 'aaaaaaad-1-blocco1_c26STAT3',
       'aaaaaaaf-1-blocco1_c26STAT3', 'aaaaaaag-1-blocco1_c26STAT3',
       'aaaaaaam-1-blocco1_c26STAT3', 'aaaaaaap-1-blocco1_c26STAT3',
       'aaaaaabb-1-blocco1_c26STAT3', 'aaaaaabd-1-blocco1_c26STAT3',
       ...
       'aaaajppo-1-blocco1_c26STAT3', 'aaaajppp-1-blocco1_c26STAT3',
       'aaaakaaa-1-blocco1_c26STAT3', 'aaaakaab-1-blocco1_c26STAT3',
       'aaaakaad-1-blocco1_c26STAT3', 'aaaakaaf-1-blocco1_c26STAT3',
       'aaaakaah-1-blocco1_c26STAT3', 'aaaakaai-1-blocco1_c26STAT3',
       'aaaakaaj-1-blocco1_c26STAT3', 'aaaakaak-1-blocco1_c26STAT3'],
      dtype='object', length=31755)