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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 1 new columns ({'layer'}) and 11 missing columns ({'region_new', 'align_y', 'Xcorr', 'Ycorr', 'idd', 'cell', 'cell_id', 'array', 'align_x', 'Unnamed: 0', 'celltype'}).
This happened while the csv dataset builder was generating data using
gzip://codex_duodenum_aligned.csv::hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_duodenum_aligned.csv.gz, ['hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_colon.csv.gz', 'hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_duodenum_aligned.csv.gz', 'hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_duodenum_raw.csv.gz', 'hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/xenium_colon.csv.gz']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1848, in _prepare_split_single
writer.write_table(table)
~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 765, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 773, in _write_table
pa_table = table_cast(pa_table, self._schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
datasets.table.CastError: Couldn't cast
x: double
y: double
layer: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 597
to
{'Unnamed: 0': Value('int64'), 'cell_id': Value('float64'), 'cell': Value('string'), 'x': Value('float64'), 'y': Value('float64'), 'Xcorr': Value('int64'), 'Ycorr': Value('int64'), 'region_new': Value('float64'), 'array': Value('string'), 'align_x': Value('int64'), 'align_y': Value('int64'), 'idd': Value('string'), 'celltype': Value('string')}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1850, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
...<4 lines>...
)
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 1 new columns ({'layer'}) and 11 missing columns ({'region_new', 'align_y', 'Xcorr', 'Ycorr', 'idd', 'cell', 'cell_id', 'array', 'align_x', 'Unnamed: 0', 'celltype'}).
This happened while the csv dataset builder was generating data using
gzip://codex_duodenum_aligned.csv::hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_duodenum_aligned.csv.gz, ['hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_colon.csv.gz', 'hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_duodenum_aligned.csv.gz', 'hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/codex_duodenum_raw.csv.gz', 'hf://datasets/a12910/spacemap-data@043a9a8505bd6decb9ae6fa0af49438e9f2ea7ba/xenium_colon.csv.gz']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Unnamed: 0 int64 | cell_id float64 | cell string | x float64 | y float64 | Xcorr int64 | Ycorr int64 | region_new float64 | array string | align_x int64 | align_y int64 | idd string | celltype string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
580,888 | 1 | B014_1.0_1.0 | 8,530 | 6,734 | 8,530 | 81,734 | 1 | S1 | 9,149 | 2,336 | S1_9149_2336 | T cells, nerve, smooth muscle, globlet, paneth |
580,889 | 4 | B014_1.0_4.0 | 4,374 | 11,883 | 4,374 | 86,883 | 1 | S1 | 5,344 | 7,291 | S1_5344_7291 | Epithelial |
580,890 | 5 | B014_1.0_5.0 | 9,050 | 12,232 | 9,050 | 87,232 | 1 | S1 | 9,926 | 7,605 | S1_9926_7605 | Nerve |
580,891 | 6 | B014_1.0_6.0 | 2,472 | 9,759 | 2,472 | 84,759 | 1 | S1 | 3,424 | 5,172 | S1_3424_5172 | Epithelial |
580,892 | 8 | B014_1.0_8.0 | 4,010 | 5,911 | 4,010 | 80,911 | 1 | S1 | 4,645 | 1,613 | S1_4645_1613 | Epithelial |
580,893 | 9 | B014_1.0_9.0 | 4,776 | 5,997 | 4,776 | 80,997 | 1 | S1 | 5,439 | 1,729 | S1_5439_1729 | Epithelial |
580,894 | 12 | B014_1.0_12.0 | 2,043 | 7,232 | 2,043 | 82,232 | 1 | S1 | 2,976 | 2,749 | S1_2976_2749 | null |
580,895 | 14 | B014_1.0_14.0 | 4,427 | 7,342 | 4,427 | 82,342 | 1 | S1 | 5,065 | 2,918 | S1_5065_2918 | endothelial/fibroblast |
580,896 | 15 | B014_1.0_15.0 | 1,293 | 9,029 | 1,293 | 84,029 | 1 | S1 | 2,254 | 4,505 | S1_2254_4505 | Epithelial |
580,897 | 18 | B014_1.0_18.0 | 4,082 | 9,006 | 4,082 | 84,006 | 1 | S1 | 4,878 | 4,526 | S1_4878_4526 | endothelial/fibroblast |
580,898 | 20 | B014_1.0_20.0 | 9,904 | 6,982 | 9,904 | 81,982 | 1 | S1 | 10,499 | 2,558 | S1_10499_2558 | endothelial/fibroblast |
580,899 | 21 | B014_1.0_21.0 | 4,946 | 15,975 | 4,946 | 90,975 | 1 | S1 | 5,961 | 11,276 | S1_5961_11276 | null |
580,900 | 22 | B014_1.0_22.0 | 11,279 | 12,630 | 11,279 | 87,630 | 1 | S1 | 12,238 | 8,007 | S1_12238_8007 | endothelial/fibroblast |
580,901 | 23 | B014_1.0_23.0 | 5,521 | 14,552 | 5,521 | 89,552 | 1 | S1 | 6,644 | 9,801 | S1_6644_9801 | Epithelial |
580,902 | 25 | B014_1.0_25.0 | 3,510 | 6,813 | 3,510 | 81,813 | 1 | S1 | 4,189 | 2,366 | S1_4189_2366 | endothelial/fibroblast |
580,903 | 26 | B014_1.0_26.0 | 5,155 | 13,272 | 5,155 | 88,272 | 1 | S1 | 6,298 | 8,565 | S1_6298_8565 | Epithelial |
580,904 | 27 | B014_1.0_27.0 | 4,810 | 11,586 | 4,810 | 86,586 | 1 | S1 | 5,799 | 6,999 | S1_5799_6999 | null |
580,905 | 29 | B014_1.0_29.0 | 4,286 | 9,903 | 4,286 | 84,903 | 1 | S1 | 5,158 | 5,387 | S1_5158_5387 | Plasma cells/Epithelial cells/Stromal |
580,906 | 30 | B014_1.0_30.0 | 5,256 | 15,362 | 5,256 | 90,362 | 1 | S1 | 6,233 | 10,647 | S1_6233_10647 | null |
580,907 | 31 | B014_1.0_31.0 | 8,041 | 12,568 | 8,041 | 87,568 | 1 | S1 | 8,910 | 7,921 | S1_8910_7921 | endothelial/fibroblast |
580,908 | 35 | B014_1.0_35.0 | 4,971 | 6,984 | 4,971 | 81,984 | 1 | S1 | 5,578 | 2,573 | S1_5578_2573 | endothelial/fibroblast |
580,909 | 36 | B014_1.0_36.0 | 4,699 | 9,792 | 4,699 | 84,792 | 1 | S1 | 5,524 | 5,265 | S1_5524_5265 | B cells |
580,910 | 37 | B014_1.0_37.0 | 3,751 | 11,980 | 3,751 | 86,980 | 1 | S1 | 4,632 | 7,414 | S1_4632_7414 | Plasma cells/Epithelial cells/Stromal |
580,911 | 38 | B014_1.0_38.0 | 4,070 | 11,812 | 4,070 | 86,812 | 1 | S1 | 4,988 | 7,233 | S1_4988_7233 | Macrophage |
580,912 | 39 | B014_1.0_39.0 | 4,969 | 14,146 | 4,969 | 89,146 | 1 | S1 | 6,154 | 9,411 | S1_6154_9411 | null |
580,913 | 42 | B014_1.0_42.0 | 8,667 | 11,970 | 8,667 | 86,970 | 1 | S1 | 9,523 | 7,347 | S1_9523_7347 | Treg |
580,914 | 44 | B014_1.0_44.0 | 4,078 | 6,072 | 4,078 | 81,072 | 1 | S1 | 4,707 | 1,753 | S1_4707_1753 | Epithelial |
580,915 | 45 | B014_1.0_45.0 | 3,724 | 6,024 | 3,724 | 81,024 | 1 | S1 | 4,364 | 1,672 | S1_4364_1672 | Fibroblast |
580,916 | 46 | B014_1.0_46.0 | 6,664 | 11,283 | 6,664 | 86,283 | 1 | S1 | 7,499 | 6,736 | S1_7499_6736 | endothelial/fibroblast |
580,917 | 47 | B014_1.0_47.0 | 10,047 | 8,074 | 10,047 | 83,074 | 1 | S1 | 10,701 | 3,538 | S1_10701_3538 | endothelial/fibroblast |
580,918 | 48 | B014_1.0_48.0 | 5,301 | 13,424 | 5,301 | 88,424 | 1 | S1 | 6,434 | 8,714 | S1_6434_8714 | Epithelial |
580,919 | 49 | B014_1.0_49.0 | 8,346 | 10,274 | 8,346 | 85,274 | 1 | S1 | 9,142 | 5,695 | S1_9142_5695 | Treg |
580,920 | 52 | B014_1.0_52.0 | 1,350 | 8,757 | 1,350 | 83,757 | 1 | S1 | 2,316 | 4,234 | S1_2316_4234 | Epithelial |
580,921 | 53 | B014_1.0_53.0 | 1,680 | 8,530 | 1,680 | 83,530 | 1 | S1 | 2,680 | 4,001 | S1_2680_4001 | null |
580,922 | 56 | B014_1.0_56.0 | 4,596 | 13,381 | 4,596 | 88,381 | 1 | S1 | 5,787 | 8,667 | S1_5787_8667 | Epithelial |
580,923 | 59 | B014_1.0_59.0 | 5,008 | 14,343 | 5,008 | 89,343 | 1 | S1 | 6,162 | 9,614 | S1_6162_9614 | null |
580,924 | 60 | B014_1.0_60.0 | 4,549 | 12,651 | 4,549 | 87,651 | 1 | S1 | 5,657 | 7,991 | S1_5657_7991 | Endothelial |
580,925 | 62 | B014_1.0_62.0 | 6,424 | 16,888 | 6,424 | 91,888 | 1 | S1 | 7,600 | 12,033 | S1_7600_12033 | null |
580,926 | 63 | B014_1.0_63.0 | 6,428 | 5,863 | 6,428 | 80,863 | 1 | S1 | 7,015 | 1,522 | S1_7015_1522 | endothelial/fibroblast |
580,927 | 64 | B014_1.0_64.0 | 5,314 | 12,924 | 5,314 | 87,924 | 1 | S1 | 6,379 | 8,258 | S1_6379_8258 | Epithelial |
580,928 | 66 | B014_1.0_66.0 | 6,088 | 16,673 | 6,088 | 91,673 | 1 | S1 | 7,228 | 11,831 | S1_7228_11831 | null |
580,929 | 69 | B014_1.0_69.0 | 1,651 | 7,216 | 1,651 | 82,216 | 1 | S1 | 2,601 | 2,701 | S1_2601_2701 | null |
580,930 | 70 | B014_1.0_70.0 | 5,681 | 13,882 | 5,681 | 88,882 | 1 | S1 | 6,791 | 9,175 | S1_6791_9175 | Goblet cells |
580,931 | 73 | B014_1.0_73.0 | 4,365 | 10,486 | 4,365 | 85,486 | 1 | S1 | 5,300 | 5,934 | S1_5300_5934 | Epithelial |
580,932 | 74 | B014_1.0_74.0 | 5,458 | 15,759 | 5,458 | 90,759 | 1 | S1 | 6,466 | 11,049 | S1_6466_11049 | null |
580,933 | 76 | B014_1.0_76.0 | 6,223 | 11,650 | 6,223 | 86,650 | 1 | S1 | 7,091 | 7,091 | S1_7091_7091 | Treg |
580,934 | 78 | B014_1.0_78.0 | 4,868 | 6,012 | 4,868 | 81,012 | 1 | S1 | 5,532 | 1,739 | S1_5532_1739 | Epithelial |
580,935 | 79 | B014_1.0_79.0 | 4,713 | 5,989 | 4,713 | 80,989 | 1 | S1 | 5,373 | 1,722 | S1_5373_1722 | Epithelial |
580,936 | 80 | B014_1.0_80.0 | 5,678 | 12,246 | 5,678 | 87,246 | 1 | S1 | 6,612 | 7,659 | S1_6612_7659 | Smooth muscle |
580,937 | 81 | B014_1.0_81.0 | 9,001 | 5,997 | 9,001 | 80,997 | 1 | S1 | 9,599 | 1,618 | S1_9599_1618 | Endothelial |
580,938 | 82 | B014_1.0_82.0 | 2,665 | 8,538 | 2,665 | 83,538 | 1 | S1 | 3,580 | 4,027 | S1_3580_4027 | Epithelial |
580,939 | 83 | B014_1.0_83.0 | 4,631 | 11,400 | 4,631 | 86,400 | 1 | S1 | 5,620 | 6,817 | S1_5620_6817 | Fibroblast |
580,940 | 84 | B014_1.0_84.0 | 3,848 | 11,131 | 3,848 | 86,131 | 1 | S1 | 4,819 | 6,550 | S1_4819_6550 | Epithelial |
580,941 | 85 | B014_1.0_85.0 | 4,014 | 12,707 | 4,014 | 87,707 | 1 | S1 | 4,993 | 8,090 | S1_4993_8090 | Macrophage |
580,942 | 87 | B014_1.0_87.0 | 2,486 | 9,367 | 2,486 | 84,367 | 1 | S1 | 3,432 | 4,804 | S1_3432_4804 | Epithelial |
580,943 | 89 | B014_1.0_89.0 | 7,884 | 7,339 | 7,884 | 82,339 | 1 | S1 | 8,544 | 2,905 | S1_8544_2905 | T cells, nerve, smooth muscle, globlet, paneth |
580,944 | 90 | B014_1.0_90.0 | 5,475 | 15,751 | 5,475 | 90,751 | 1 | S1 | 6,485 | 11,040 | S1_6485_11040 | Epithelial |
580,945 | 91 | B014_1.0_91.0 | 5,324 | 15,116 | 5,324 | 90,116 | 1 | S1 | 6,336 | 10,379 | S1_6336_10379 | Plasma cells/Epithelial cells/Stromal |
580,946 | 92 | B014_1.0_92.0 | 5,292 | 16,438 | 5,292 | 91,438 | 1 | S1 | 6,366 | 11,695 | S1_6366_11695 | Endothelial |
580,947 | 93 | B014_1.0_93.0 | 3,134 | 9,172 | 3,134 | 84,172 | 1 | S1 | 4,009 | 4,663 | S1_4009_4663 | Epithelial |
580,948 | 95 | B014_1.0_95.0 | 7,100 | 16,951 | 7,100 | 91,951 | 1 | S1 | 8,260 | 12,121 | S1_8260_12121 | endothelial/fibroblast |
580,949 | 96 | B014_1.0_96.0 | 10,967 | 12,441 | 10,967 | 87,441 | 1 | S1 | 11,920 | 7,821 | S1_11920_7821 | endothelial/fibroblast |
580,950 | 99 | B014_1.0_99.0 | 4,957 | 13,287 | 4,957 | 88,287 | 1 | S1 | 6,134 | 8,571 | S1_6134_8571 | null |
580,951 | 102 | B014_1.0_102.0 | 1,195 | 8,365 | 1,195 | 83,365 | 1 | S1 | 2,134 | 3,854 | S1_2134_3854 | Epithelial |
580,952 | 103 | B014_1.0_103.0 | 4,505 | 9,571 | 4,505 | 84,571 | 1 | S1 | 5,326 | 5,057 | S1_5326_5057 | B cells |
580,953 | 104 | B014_1.0_104.0 | 11,613 | 13,923 | 11,613 | 88,923 | 1 | S1 | 12,614 | 9,223 | S1_12614_9223 | endothelial/fibroblast |
580,954 | 105 | B014_1.0_105.0 | 5,855 | 14,308 | 5,855 | 89,308 | 1 | S1 | 6,958 | 9,579 | S1_6958_9579 | Endothelial |
580,955 | 107 | B014_1.0_107.0 | 3,942 | 6,045 | 3,942 | 81,045 | 1 | S1 | 4,575 | 1,717 | S1_4575_1717 | Epithelial |
580,956 | 108 | B014_1.0_108.0 | 4,787 | 13,367 | 4,787 | 88,367 | 1 | S1 | 5,984 | 8,644 | S1_5984_8644 | Epithelial |
580,957 | 109 | B014_1.0_109.0 | 6,124 | 17,285 | 6,124 | 92,285 | 1 | S1 | 7,283 | 12,426 | S1_7283_12426 | Epithelial |
580,958 | 111 | B014_1.0_111.0 | 10,195 | 8,150 | 10,195 | 83,150 | 1 | S1 | 10,861 | 3,601 | S1_10861_3601 | endothelial/fibroblast |
580,959 | 113 | B014_1.0_113.0 | 11,909 | 15,198 | 11,909 | 90,198 | 1 | S1 | 13,007 | 10,412 | S1_13007_10412 | endothelial/fibroblast |
580,960 | 114 | B014_1.0_114.0 | 3,732 | 11,470 | 3,732 | 86,470 | 1 | S1 | 4,666 | 6,889 | S1_4666_6889 | Epithelial |
580,961 | 116 | B014_1.0_116.0 | 5,633 | 14,252 | 5,633 | 89,252 | 1 | S1 | 6,765 | 9,517 | S1_6765_9517 | Epithelial |
580,962 | 117 | B014_1.0_117.0 | 4,840 | 9,799 | 4,840 | 84,799 | 1 | S1 | 5,659 | 5,272 | S1_5659_5272 | B cells |
580,963 | 122 | B014_1.0_122.0 | 2,299 | 7,278 | 2,299 | 82,278 | 1 | S1 | 3,197 | 2,805 | S1_3197_2805 | Epithelial |
580,964 | 123 | B014_1.0_123.0 | 4,834 | 9,953 | 4,834 | 84,953 | 1 | S1 | 5,666 | 5,417 | S1_5666_5417 | B cells |
580,965 | 124 | B014_1.0_124.0 | 6,375 | 17,915 | 6,375 | 92,915 | 1 | S1 | 7,586 | 13,095 | S1_7586_13095 | Epithelial |
580,966 | 127 | B014_1.0_127.0 | 3,958 | 7,984 | 3,958 | 82,984 | 1 | S1 | 4,692 | 3,541 | S1_4692_3541 | endothelial/fibroblast |
580,967 | 128 | B014_1.0_128.0 | 3,636 | 10,641 | 3,636 | 85,641 | 1 | S1 | 4,582 | 6,068 | S1_4582_6068 | Epithelial |
580,968 | 129 | B014_1.0_129.0 | 3,998 | 10,421 | 3,998 | 85,421 | 1 | S1 | 4,951 | 5,870 | S1_4951_5870 | Epithelial |
580,969 | 130 | B014_1.0_130.0 | 9,422 | 5,634 | 9,422 | 80,634 | 1 | S1 | 9,993 | 1,245 | S1_9993_1245 | Smooth muscle/CD138/Epithelial/ |
580,970 | 132 | B014_1.0_132.0 | 8,151 | 13,185 | 8,151 | 88,185 | 1 | S1 | 9,055 | 8,530 | S1_9055_8530 | T cells, nerve, smooth muscle, globlet, paneth |
580,971 | 138 | B014_1.0_138.0 | 1,413 | 8,203 | 1,413 | 83,203 | 1 | S1 | 2,382 | 3,693 | S1_2382_3693 | Epithelial |
580,972 | 142 | B014_1.0_142.0 | 4,498 | 10,687 | 4,498 | 85,687 | 1 | S1 | 5,445 | 6,130 | S1_5445_6130 | Epithelial |
580,973 | 143 | B014_1.0_143.0 | 9,884 | 14,487 | 9,884 | 89,487 | 1 | S1 | 10,866 | 9,729 | S1_10866_9729 | Treg |
580,974 | 144 | B014_1.0_144.0 | 5,280 | 16,821 | 5,280 | 91,821 | 1 | S1 | 6,380 | 12,036 | S1_6380_12036 | Fibroblast |
580,975 | 145 | B014_1.0_145.0 | 2,550 | 8,517 | 2,550 | 83,517 | 1 | S1 | 3,484 | 4,002 | S1_3484_4002 | endothelial/fibroblast |
580,976 | 146 | B014_1.0_146.0 | 1,862 | 10,342 | 1,862 | 85,342 | 1 | S1 | 2,827 | 5,763 | S1_2827_5763 | null |
580,977 | 148 | B014_1.0_148.0 | 2,173 | 9,847 | 2,173 | 84,847 | 1 | S1 | 3,150 | 5,251 | S1_3150_5251 | null |
580,978 | 151 | B014_1.0_151.0 | 5,290 | 13,388 | 5,290 | 88,388 | 1 | S1 | 6,421 | 8,680 | S1_6421_8680 | Epithelial |
580,979 | 153 | B014_1.0_153.0 | 4,869 | 14,903 | 4,869 | 89,903 | 1 | S1 | 5,879 | 10,185 | S1_5879_10185 | null |
580,980 | 154 | B014_1.0_154.0 | 10,235 | 16,997 | 10,235 | 91,997 | 1 | S1 | 11,289 | 12,162 | S1_11289_12162 | Endothelial |
580,981 | 155 | B014_1.0_155.0 | 8,481 | 6,476 | 8,481 | 81,476 | 1 | S1 | 9,091 | 2,093 | S1_9091_2093 | Treg |
580,982 | 157 | B014_1.0_157.0 | 5,939 | 18,067 | 5,939 | 93,067 | 1 | S1 | 7,138 | 13,248 | S1_7138_13248 | null |
580,983 | 160 | B014_1.0_160.0 | 6,468 | 17,631 | 6,468 | 92,631 | 1 | S1 | 7,671 | 12,797 | S1_7671_12797 | Smooth muscle |
580,984 | 162 | B014_1.0_162.0 | 10,584 | 11,446 | 10,584 | 86,446 | 1 | S1 | 11,496 | 6,869 | S1_11496_6869 | endothelial/fibroblast |
580,985 | 164 | B014_1.0_164.0 | 3,837 | 9,042 | 3,837 | 84,042 | 1 | S1 | 4,653 | 4,568 | S1_4653_4568 | Endothelial |
580,986 | 169 | B014_1.0_169.0 | 5,741 | 14,288 | 5,741 | 89,288 | 1 | S1 | 6,858 | 9,554 | S1_6858_9554 | null |
580,987 | 170 | B014_1.0_170.0 | 8,169 | 7,991 | 8,169 | 82,991 | 1 | S1 | 8,847 | 3,527 | S1_8847_3527 | T cells, nerve, smooth muscle, globlet, paneth |
End of preview.
Space-map example datasets
Serial-section single-cell coordinate datasets used with Space-map for atlas-level 3D reconstruction. Each file is a gzipped CSV of cell coordinates with a per-section layer label.
| File | Platform / tissue | Layer column | Coord columns | Layers |
|---|---|---|---|---|
xenium_colon.csv.gz |
Xenium (transcriptomics), colon | layer (1–20) |
x, y |
20 |
codex_colon.csv.gz |
CODEX (proteomics), colon | array (S1–S16) |
x, y |
16 |
codex_duodenum_raw.csv.gz |
CODEX (proteomics), duodenum — raw | index (S1–S16) |
raw_x, raw_y |
16 |
codex_duodenum_aligned.csv.gz |
CODEX duodenum — reference aligned | layer (S1–S16) |
x, y |
16 |
Notes:
xenium_colon.csv.gzlayer labels were renumbered to a contiguous 1–20 range.- The two
codex_duodenum_*files share row order and layer labels:rawholds the input coordinates,alignedholds a reference alignment for comparison. - Additional columns (e.g.
cell_type,cell_id) are preserved where present.
Usage
from huggingface_hub import hf_hub_download
import pandas as pd
path = hf_hub_download("a12910/spacemap-data", "xenium_colon.csv.gz",
repo_type="dataset")
df = pd.read_csv(path)
See the Space-map repository for registration examples
(examples/run_platforms.py).
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