Dataset Viewer
The dataset viewer is not available for this split.
Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code: StreamingRowsError
Exception: CastError
Message: Couldn't cast
shape: list<item: int64>
child 0, item: int64
data_type: string
chunk_grid: struct<name: string, configuration: struct<chunk_shape: list<item: int64>>>
child 0, name: string
child 1, configuration: struct<chunk_shape: list<item: int64>>
child 0, chunk_shape: list<item: int64>
child 0, item: int64
chunk_key_encoding: struct<name: string, configuration: struct<separator: string>>
child 0, name: string
child 1, configuration: struct<separator: string>
child 0, separator: string
fill_value: int64
codecs: list<item: struct<name: string, configuration: struct<endian: string, level: int64, checksum: bool>> (... 1 chars omitted)
child 0, item: struct<name: string, configuration: struct<endian: string, level: int64, checksum: bool>>
child 0, name: string
child 1, configuration: struct<endian: string, level: int64, checksum: bool>
child 0, endian: string
child 1, level: int64
child 2, checksum: bool
attributes: struct<>
dimension_names: list<item: string>
child 0, item: string
zarr_format: int64
node_type: string
storage_transformers: list<item: null>
child 0, item: null
name: string
@context: struct<@language: string, @vocab: string, citeAs: string, column: string, conformsTo: string, cr: st (... 615 chars omitted)
child 0, @language: string
child 1, @vocab: string
child 2, citeAs: string
child 3, column: string
child 4, conformsTo: string
child 5, cr: string
child 6, rai: string
child 7, d
...
Object: string
child 16, fileSet: string
child 17, format: string
child 18, includes: string
child 19, isLiveDataset: string
child 20, jsonPath: string
child 21, key: string
child 22, md5: string
child 23, parentField: string
child 24, path: string
child 25, recordSet: string
child 26, references: string
child 27, regex: string
child 28, repeated: string
child 29, replace: string
child 30, samplingRate: string
child 31, sc: string
child 32, separator: string
child 33, source: string
child 34, subField: string
child 35, transform: string
license: string
description: string
conformsTo: string
@type: string
citeAs: string
datePublished: timestamp[s]
keywords: list<item: string>
child 0, item: string
distribution: list<item: struct<@type: string, @id: string, name: string, description: string, contentUrl: string, (... 93 chars omitted)
child 0, item: struct<@type: string, @id: string, name: string, description: string, contentUrl: string, encodingFo (... 81 chars omitted)
child 0, @type: string
child 1, @id: string
child 2, name: string
child 3, description: string
child 4, contentUrl: string
child 5, encodingFormat: string
child 6, sha256: string
child 7, containedIn: struct<@id: string>
child 0, @id: string
child 8, includes: string
url: string
creator: struct<@type: string, name: string, url: string>
child 0, @type: string
child 1, name: string
child 2, url: string
to
{'@context': {'@language': Value('string'), '@vocab': Value('string'), 'citeAs': Value('string'), 'column': Value('string'), 'conformsTo': Value('string'), 'cr': Value('string'), 'rai': Value('string'), 'data': {'@id': Value('string'), '@type': Value('string')}, 'dataType': {'@id': Value('string'), '@type': Value('string')}, 'dct': Value('string'), 'equivalentProperty': Value('string'), 'examples': {'@id': Value('string'), '@type': Value('string')}, 'extract': Value('string'), 'field': Value('string'), 'fileProperty': Value('string'), 'fileObject': Value('string'), 'fileSet': Value('string'), 'format': Value('string'), 'includes': Value('string'), 'isLiveDataset': Value('string'), 'jsonPath': Value('string'), 'key': Value('string'), 'md5': Value('string'), 'parentField': Value('string'), 'path': Value('string'), 'recordSet': Value('string'), 'references': Value('string'), 'regex': Value('string'), 'repeated': Value('string'), 'replace': Value('string'), 'samplingRate': Value('string'), 'sc': Value('string'), 'separator': Value('string'), 'source': Value('string'), 'subField': Value('string'), 'transform': Value('string')}, '@type': Value('string'), 'name': Value('string'), 'description': Value('string'), 'conformsTo': Value('string'), 'citeAs': Value('string'), 'creator': {'@type': Value('string'), 'name': Value('string'), 'url': Value('string')}, 'datePublished': Value('timestamp[s]'), 'keywords': List(Value('string')), 'license': Value('string'), 'url': Value('string'), 'distribution': List({'@type': Value('string'), '@id': Value('string'), 'name': Value('string'), 'description': Value('string'), 'contentUrl': Value('string'), 'encodingFormat': Value('string'), 'sha256': Value('string'), 'containedIn': {'@id': Value('string')}, 'includes': Value('string')})}
because column names don't match
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/utils.py", line 99, in get_rows_or_raise
return get_rows(
^^^^^^^^^
File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/utils.py", line 77, in get_rows
rows_plus_one = list(itertools.islice(ds, rows_max_number + 1))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2690, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2227, in __iter__
for key, pa_table in self._iter_arrow():
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2251, in _iter_arrow
for key, pa_table in self.ex_iterable._iter_arrow():
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 494, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 384, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 299, in _generate_tables
self._cast_table(pa_table, json_field_paths=json_field_paths),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 128, in _cast_table
pa_table = table_cast(pa_table, self.info.features.arrow_schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
shape: list<item: int64>
child 0, item: int64
data_type: string
chunk_grid: struct<name: string, configuration: struct<chunk_shape: list<item: int64>>>
child 0, name: string
child 1, configuration: struct<chunk_shape: list<item: int64>>
child 0, chunk_shape: list<item: int64>
child 0, item: int64
chunk_key_encoding: struct<name: string, configuration: struct<separator: string>>
child 0, name: string
child 1, configuration: struct<separator: string>
child 0, separator: string
fill_value: int64
codecs: list<item: struct<name: string, configuration: struct<endian: string, level: int64, checksum: bool>> (... 1 chars omitted)
child 0, item: struct<name: string, configuration: struct<endian: string, level: int64, checksum: bool>>
child 0, name: string
child 1, configuration: struct<endian: string, level: int64, checksum: bool>
child 0, endian: string
child 1, level: int64
child 2, checksum: bool
attributes: struct<>
dimension_names: list<item: string>
child 0, item: string
zarr_format: int64
node_type: string
storage_transformers: list<item: null>
child 0, item: null
name: string
@context: struct<@language: string, @vocab: string, citeAs: string, column: string, conformsTo: string, cr: st (... 615 chars omitted)
child 0, @language: string
child 1, @vocab: string
child 2, citeAs: string
child 3, column: string
child 4, conformsTo: string
child 5, cr: string
child 6, rai: string
child 7, d
...
Object: string
child 16, fileSet: string
child 17, format: string
child 18, includes: string
child 19, isLiveDataset: string
child 20, jsonPath: string
child 21, key: string
child 22, md5: string
child 23, parentField: string
child 24, path: string
child 25, recordSet: string
child 26, references: string
child 27, regex: string
child 28, repeated: string
child 29, replace: string
child 30, samplingRate: string
child 31, sc: string
child 32, separator: string
child 33, source: string
child 34, subField: string
child 35, transform: string
license: string
description: string
conformsTo: string
@type: string
citeAs: string
datePublished: timestamp[s]
keywords: list<item: string>
child 0, item: string
distribution: list<item: struct<@type: string, @id: string, name: string, description: string, contentUrl: string, (... 93 chars omitted)
child 0, item: struct<@type: string, @id: string, name: string, description: string, contentUrl: string, encodingFo (... 81 chars omitted)
child 0, @type: string
child 1, @id: string
child 2, name: string
child 3, description: string
child 4, contentUrl: string
child 5, encodingFormat: string
child 6, sha256: string
child 7, containedIn: struct<@id: string>
child 0, @id: string
child 8, includes: string
url: string
creator: struct<@type: string, name: string, url: string>
child 0, @type: string
child 1, name: string
child 2, url: string
to
{'@context': {'@language': Value('string'), '@vocab': Value('string'), 'citeAs': Value('string'), 'column': Value('string'), 'conformsTo': Value('string'), 'cr': Value('string'), 'rai': Value('string'), 'data': {'@id': Value('string'), '@type': Value('string')}, 'dataType': {'@id': Value('string'), '@type': Value('string')}, 'dct': Value('string'), 'equivalentProperty': Value('string'), 'examples': {'@id': Value('string'), '@type': Value('string')}, 'extract': Value('string'), 'field': Value('string'), 'fileProperty': Value('string'), 'fileObject': Value('string'), 'fileSet': Value('string'), 'format': Value('string'), 'includes': Value('string'), 'isLiveDataset': Value('string'), 'jsonPath': Value('string'), 'key': Value('string'), 'md5': Value('string'), 'parentField': Value('string'), 'path': Value('string'), 'recordSet': Value('string'), 'references': Value('string'), 'regex': Value('string'), 'repeated': Value('string'), 'replace': Value('string'), 'samplingRate': Value('string'), 'sc': Value('string'), 'separator': Value('string'), 'source': Value('string'), 'subField': Value('string'), 'transform': Value('string')}, '@type': Value('string'), 'name': Value('string'), 'description': Value('string'), 'conformsTo': Value('string'), 'citeAs': Value('string'), 'creator': {'@type': Value('string'), 'name': Value('string'), 'url': Value('string')}, 'datePublished': Value('timestamp[s]'), 'keywords': List(Value('string')), 'license': Value('string'), 'url': Value('string'), 'distribution': List({'@type': Value('string'), '@id': Value('string'), 'name': Value('string'), 'description': Value('string'), 'contentUrl': Value('string'), 'encodingFormat': Value('string'), 'sha256': Value('string'), 'containedIn': {'@id': Value('string')}, 'includes': Value('string')})}
because column names don't matchNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
BBBC032 as OME-Zarr
An exploration of converting a benchmarking CC0 dataset in TIFF to OME-Zarr.
This is the metadata of the dataset in the original website:
Mouse embryo blastocyst cells
Segmenting nuclei in 3D images can be challenging especially when nuclei are clustered not only in XY plane but also in XZ and YZ planes. Manually annotated ground truth provides a reference for image analysis software testing purposes. These images of mouse embryo blastocyst cells also have changing nuclei intensity in Z plane which makes finding the right threshold for successful segmentation a difficult task. This image set also contains GAPDH transcripts that can be quantified in each cell. Images
Images acquired by using PerkinElmer Ultraview VoX spinning disk microscope combined with a Leica SP8 with a 63x immersion objective (Distance between Z-slices = 0.5 um)
These images were generated by the Laboratory for Modeling Development and Regeneration at Hubrecht Institute, The Netherlands. Please contact Nicolas Rivron and/or Javier Frias Aldeguer for more information.
To the extent possible under law, Nicolas Rivron has waived all copyright and related or neighboring rights to BBBC032v1.
647 channel (BMP4blastocystC0): BMP4 transcripts 568 channel (BMP4blastocystC1): GAPDH transcripts 488 channel (BMP4blastocystC2): WGA 405 channel (BMP4blastocystC3): Hoechst Width = 103.424 microns (1024) Height = 135.744 microns (1344) Depth = 86 microns (172)
Original citation
"We used image set BBBC032v1 Rivron et al. 2018, available from the Broad Bioimage Benchmark Collection Ljosa et al., Nature Methods, 2012."
Detail
- source: https://bbbc.broadinstitute.org/BBBC032
- conversion: https://github.com/lubianat/bbbc032_to_zarr
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