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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1531, in _prepare_split_single
for key, record in generator:
^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
for item in generator(*args, **kwargs):
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 127, in _generate_examples
for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
for filename, f in tar_iterator:
^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
for x in self.generator(*self.args):
~~~~~~~~~~~~~~^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1405, in _iter_from_urlpath
with xopen(urlpath, "rb", download_config=download_config, block_size=0) as f:
~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 982, in xopen
file_obj = fs.open(paths[0], mode)
File "<string>", line 3, in open
File "/usr/local/lib/python3.14/unittest/mock.py", line 1176, in __call__
return self._mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1180, in _mock_call
return self._execute_mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1247, in _execute_mock_call
result = effect(*args, **kwargs)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 786, in wrapped
tracker.files[urlpath] = {"read": 0, "size": int(f.size)}
~~~^^^^^^^^
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
The above exception was the direct cause of the following exception:
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 1393, 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 1571, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
png image | __key__ string | __url__ string |
|---|---|---|
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_10_38 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_10_47 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_10_52 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_10_6 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_12_1 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_12_12 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_12_37 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_13_120 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_13_14 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_13_53 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_14_11 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_14_13 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_14_16 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_14_33 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_15_52 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_15_62 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_15_75 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_16_101 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_16_118 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_16_35 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_16_80 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_1_13 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_1_32 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_1_74 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_2_17 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_2_45 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_2_48 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_2_61 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_2_8 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_3_36 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_4_31 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_4_38 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_4_46 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_4_48 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_4_59 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_4_9 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_5_31 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_5_59 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_10 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_13 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_27 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_4 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_48 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_60 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_75 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_6_86 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_7_14 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_7_64 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_8_40 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_8_60 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_8_78 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_9_15 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_9_21 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_9_33 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_9_47 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_9_65 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A01/cell_png/plate1_A01_9_99 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_18 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_2 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_20 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_34 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_37 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_39 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_41 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_49 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_57 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_10_65 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_1 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_11 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_16 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_18 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_21 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_22 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_25 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_32 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_37 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_43 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_44 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_46 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_47 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_52 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_11_60 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_13 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_14 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_19 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_20 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_27 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_29 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_40 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_69 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_12_70 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_10 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_102 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_21 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_24 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_25 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_32 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_44 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_49 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar | |
data/multiple_nucleus/multiple_pathogens/plate1_A02/cell_png/plate1_A02_13_56 | hf://datasets/einarolafsson/spacr-example-screen@187794004ff1273de0af0e997a2c9eca737fb7c9/plate1-data.tar |
End of preview.
spaCR example screen — GFP-TSG101 recruitment
The published pooled CRISPR-Cas9 screen that spaCR's Regression module and
its documentation use as the reference example: HeLa cells expressing
GFP-TSG101, infected with a pooled Toxoplasma gondii knockout library, four
384-well plates. The screen's controls are SAG1 (TGGT1_233460, negative)
and GRA14 (TGGT1_239740, positive: its loss removes TSG101 recruitment to
the parasitophorous vacuole).
Each plate is split into two separately downloadable archives, so a user can
fetch the measurements without the crops. spaCR's Regression screen lists
them with their sizes (spacr.screen_data).
Files
| file | bytes | contents |
|---|---|---|
plate1-measurements.tar |
555,673,600 | measurements/measurements.db |
plate2-measurements.tar |
530,165,760 | measurements/measurements.db |
plate3-measurements.tar |
513,576,960 | measurements/measurements.db |
plate4-measurements.tar |
455,454,720 | measurements/measurements.db |
plate1-data.tar |
8,874,557,440 | data/ single-cell PNG crops |
plate2-data.tar |
8,403,578,880 | data/ single-cell PNG crops |
plate3-data.tar |
8,040,058,880 | data/ single-cell PNG crops |
plate4-data.tar |
7,375,370,240 | data/ single-cell PNG crops |
All archives are uncompressed tars whose members are relative to a plate folder; unpack the two archives of one plate into the same folder.
measurements/measurements.db
A spaCR Measure SQLite database with the tables cell, cytoplasm,
nucleus, pathogen (per-object morphology, intensity, texture and
colocalisation features, keyed by plateID, rowID, columnID, fieldID
and object label), png_list (one row per crop: png_path, prcfo object
key) and settings (the Measure settings used). Plate 1, for scale: 60,816
cells in 342 wells, 80,889 nuclei, 111,317 pathogen objects. Crop paths in
png_list are relative (data/...).
data/
224 x 224 px PNG crops of single cells (Measure crop_mode cell, image
channels 0-2), sorted by object composition into
data/{single,multiple}_nucleus/{single,multiple}_pathogen(s)/plate<N>_<well>/cell_png/plate<N>_<well>_<field>_<object>.png.
The stitched merged/ image stacks (about 300 GB per plate) are not
published here. The per-cell classifier scores (plate<N>_dv.csv) and the
per-well guide read counts (plate_<N>_unique_combinations.csv) are
distributed with the spaCR example-data release.
A 28 MB cut of plate 1 with a Regression run made from it is published as einarolafsson/spacr-example-hit.
Licence and attribution
CC BY 4.0. When you use these data, please credit the TSG101 recruitment screen (Olafsson EB et al., this dataset, einarolafsson/spacr-example-screen) and cite spaCR:
- Olafsson EB, Arnold C-S, Kellermeier JA, Rimple PA, Kaur H, Wang Y, Sexton JZ, Svärd S, Carruthers VB, O'Meara MJ. spaCR: spatial phenotype analysis of CRISPR-Cas9 screens. Zenodo. doi:10.5281/zenodo.21343316
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