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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 17138 new columns ({'AP3B2', 'RP11-96L14.7', 'SMARCA4', 'NAA20', 'ZNF117', 'CCM2L', 'TBCC', 'KCNMB2-AS1', 'ACSM6', 'HAS3', 'TWF2', 'ZDHHC19', 'CACNA1C', 'YWHAE', 'CLN6', 'CCDC57', 'TAS2R5', 'PFDN2', 'SHANK2', 'GATA6', 'RACK1', 'IPMK', 'KIF5C', 'IGFBP2', 'RHOT2', 'THAP12', 'SERPINI2', 'ZNF229', 'MAPKAPK2', 'RFTN1', 'ARL9', 'GAPT', 'TAS2R20', 'FAM49B', 'PEX16', 'MYLIP', 'CYP2D6', 'ITM2C', 'ATP5J2', 'OR2A1-AS1', 'CXorf56', 'SLX1B', 'MRPL13', 'HP1BP3', 'TMEM115', 'PHB2', 'TRPV2', 'FAAP24', 'LCE6A', 'MAPK8IP2', 'SERPINB1', 'C5orf45', 'CTD-2007L18.5', 'TRIAP1', 'EXO1', 'REEP2', 'MSRB3', 'TMEM52', 'MRPL39', 'FAM156A', 'TRIM44', 'ZNF558', 'IDE', 'MATR3', 'ALDH16A1', 'SORBS3', 'ATPAF1', 'TGFBI', 'CPAMD8', 'IL15', 'CLHC1', 'CLEC12B', 'LRP11', 'SLC52A2', 'RP11-226E21.4', 'ZNF784', 'TMBIM6', 'SPERT', 'VIP', 'C2CD2', 'VGLL4', 'BMX', 'PPP1R3B', 'HNRNPH2', 'DSC2', 'BZW2', 'INPPL1', 'NPIPB11', 'RP11-679C8.2', 'ATP6V1A', 'CCDC120', 'KRT13', 'TBC1D1', 'LINGO2', 'PPP1R15B', 'UBA5', 'TMEM233', 'LRIF1', 'FAM131C', 'COIL', 'CRISPLD2', 'S100A8', 'PPEF1', 'ZNHIT3', 'TTYH1', 'FAM60A', 'H1FX', 'SGIP1', 'TM4SF18', 'ALKBH5', 'BEND6', 'PHB', 'STIM1', 'JUNB', 'IL32', 'LY6D', 'LINC01181', 'RPL41', 'TMED3', 'RGPD1', 'RP11-223P11.3', 'ATP12A', 'ALDH1A1', 'CDK5RAP1', 'TACC3', 'CIAPIN1', 'ASGR1', 'PLA2G4B', 'MREG', 'DUSP3', 'DUSP16', 'MIR1199', 'GALNT3', 'CCR5', 'SLC25A29', 'C7orf55', 'NCAPG', 'LIPE-AS1', 'SDF2', 'MSL2', 'TBC1D8', 'TREML1', 'ADHFE1', 'CHRDL1', 'CCND1', 'IL36G', 'C14orf166', 'SFTPD-AS1', 'PSMB7', 'CCS', 'KRT18', 
...
', 'PNPLA5', 'NUDT19', 'SRR', 'NPTXR', 'USP20', 'ADAM15', 'COX5B', 'PSENEN', 'HOXC4', 'ATAD5', 'C1orf228', 'STRA6', 'GMIP', 'RP1-71H19.2', 'TMEM184A', 'ZNF837', 'CCDC171', 'ASUN', 'TMEM59L', 'ERGIC3', 'DNAJB5', 'SLCO3A1', 'APITD1', 'RASA4', 'KIDINS220', 'ORAI3', 'FCRL1', 'HABP4', 'LA16c-385E7.1', 'HOXD3', 'PSMD6', 'PCDHGC3', 'NXT1', 'RBM43', 'DNASE1', 'LPAR1', 'VMO1', 'ACADVL', 'POLR3A', 'DEFB106A', 'MRVI1', 'CDK6', 'QTRT1', 'AP3S2', 'EFCAB10', 'TXNDC8', 'ZC3H13', 'AGPAT3', 'CDH18', 'PSMD11', 'SON', 'PLCL2', 'OBSL1', 'IL1RL2', 'PLA2G4A', 'RP11-2C24.9', 'SYT10', 'SMAD6', 'RP11-342C20.2', 'LDHB', 'CCDC81', 'KPTN', 'GEMIN7', 'NUDCD1', 'ANKRD23', 'NEMF', 'GATSL2', 'TRIM8', 'UHRF1', 'CLIC6', 'RCOR3', 'MYCL', 'SPACA6', 'DSEL', 'TCF3', 'EGR3', 'CERCAM', 'TCTN2', 'NPEPPS', 'LINC00998', 'AHNAK2', 'ARIH2', 'EAPP', 'VWC2', 'ATP6V1E2', 'ALG9', 'ITPKC', 'FAM188B', 'STX1A', 'KALRN', 'TMEM40', 'TNFAIP8L2', 'KIF11', 'RP11-982M15.2', 'LMAN2L', 'CTC-518B2.12', 'CORO2A', 'CCDC170', 'CASP7', 'TNPO1', 'CA5B', 'GALNT14', 'PROCA1', 'PCDHB4', 'PUSL1', 'PLAC1', 'ZNF680', 'DOCK1', 'ZDHHC15', 'LRRC39', 'RXFP1', 'AMOTL1', 'GOLGA6L4', 'RRBP1', 'KDM4C', 'CHMP6', 'RP11-368I7.4', 'ALPK3', 'IRAK4', 'PEBP1', 'ACTR2', 'RPRD1B', 'RP3-402G11.26', 'UNC5A', 'CYB561D1', 'AC104024.1', 'LIMS3', 'TLE2', 'TRIM26', 'KIAA1551', 'AIG1', 'DUSP8', 'PPP2R2D', 'USP36', 'KCNIP4', 'MID2', 'HIST1H1E', 'ARHGAP40', 'NAA15', 'DDX58', 'CAPN1', 'CAMK2B', 'FAM188A', 'SIN3B', 'TMED5', 'PRR26', 'OGFOD1', 'BEX3', 'CAPG', 'TPCN1', 'RPA2'}) and 3 missing columns ({'yaxis', 'xaxis', 'r'}).

This happened while the csv dataset builder was generating data using

hf://datasets/jiawennnn/STimage-1K4M/ST/gene_exp/GSE144239_GSM4284316_count.csv (at revision 1c2a89874eed9bb70606373d2b7551c9583a0131)

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 "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1870, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 622, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2292, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2240, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Unnamed: 0: string
              MIR1302-2: double
              RP11-34P13.7: double
              RP11-34P13.14: double
              FO538757.1: double
              RP4-669L17.10: double
              RP11-206L10.9: double
              LINC00115: double
              RP11-54O7.1: double
              SAMD11: double
              NOC2L: double
              KLHL17: double
              PLEKHN1: double
              PERM1: double
              HES4: double
              ISG15: double
              AGRN: double
              RNF223: double
              C1orf159: double
              TTLL10: double
              TNFRSF18: double
              TNFRSF4: double
              SDF4: double
              B3GALT6: double
              FAM132A: double
              UBE2J2: double
              SCNN1D: double
              ACAP3: double
              PUSL1: double
              CPSF3L: double
              CPTP: double
              TAS1R3: double
              DVL1: double
              MXRA8: double
              AURKAIP1: double
              CCNL2: double
              MRPL20: double
              RP4-758J18.13: double
              ANKRD65: double
              VWA1: double
              ATAD3C: double
              ATAD3B: double
              ATAD3A: double
              TMEM240: double
              SSU72: double
              FNDC10: double
              MIB2: double
              MMP23B: double
              CDK11B: double
              SLC35E2B: double
              CDK11A: double
              SLC35E2: double
              NADK: double
              GNB1: double
              RP1-140A9.1: double
              CALML6: double
              TMEM52: double
              CFAP74: double
              GABRD: double
              PRKCZ: double
              FAAP20: double
              SKI: double
              MORN1: double
              RER1: double
              PEX10: double
              PLCH2: double
              PANK4: double
              HES5: double
              TNFRSF14: double
              MMEL1: double
              FAM213B: double
              TTC34: double
              PRDM16: double
              ARHGEF16: double
              MEGF6: double
              RP11-46F15.2: double
              TPRG1L: double
              WRAP73: double
              TP73: double
              SMIM1: double
              LRRC47: double
              CEP104: double
              DFFB: double
              C1orf174: double
              AJAP1: double
              NPHP4: double
              KCNAB2: double
              RP1-120G22.11: double
              RPL22: double
              RNF207: double
              ICMT: double
              GPR153: double
              ACOT7: double
              HES2: double
              ESPN: double
              TNFRSF25: double
              PLEKHG5: double
              NOL9: 
              ...
              e
              NSDHL: double
              ZNF185: double
              PNMA3: double
              PNMA6A: double
              LL0XNC01-16G2.1: double
              ZNF275: double
              ZFP92: double
              TREX2: double
              HAUS7: double
              BGN: double
              FAM58A: double
              DUSP9: double
              SLC6A8: double
              BCAP31: double
              ABCD1: double
              SRPK3: double
              IDH3G: double
              SSR4: double
              PDZD4: double
              AVPR2: double
              L1CAM: double
              ARHGAP4: double
              NAA10: double
              RENBP: double
              HCFC1: double
              TMEM187: double
              IRAK1: double
              MECP2: double
              TKTL1: double
              FLNA: double
              EMD: double
              DNASE1L1: double
              RPL10: double
              TAZ: double
              ATP6AP1: double
              GDI1: double
              FAM50A: double
              PLXNA3: double
              LAGE3: double
              UBL4A: double
              SLC10A3: double
              FAM3A: double
              G6PD: double
              IKBKG: double
              CTAG1A: double
              CTAG1B: double
              CTAG2: double
              GAB3: double
              DKC1: double
              MPP1: double
              H2AFB1: double
              F8A1: double
              F8: double
              FUNDC2: double
              BRCC3: double
              MTCP1: double
              VBP1: double
              CLIC2: double
              H2AFB2: double
              F8A2: double
              F8A3: double
              H2AFB3: double
              TMLHE: double
              SPRY3: double
              VAMP7: double
              IL9R: double
              RPS4Y1: double
              ZFY: double
              LINC00278: double
              PCDH11Y: double
              TBL1Y: double
              USP9Y: double
              DDX3Y: double
              UTY: double
              TMSB4Y: double
              NLGN4Y: double
              FAM224B: double
              FAM224A: double
              HSFY1: double
              HSFY2: double
              TTTY14: double
              KDM5D: double
              EIF1AY: double
              RPS4Y2: double
              BPY2: double
              DAZ1: double
              DAZ2: double
              AC012005.2: double
              AC012005.1: double
              BPY2B: double
              DAZ3: double
              DAZ4: double
              BPY2C: double
              AC006386.1: double
              LINC00266-4P: double
              AC006328.1: double
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1929671
              to
              {'Unnamed: 0': Value(dtype='string', id=None), 'yaxis': Value(dtype='float64', id=None), 'xaxis': Value(dtype='float64', id=None), 'r': Value(dtype='float64', id=None)}
              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 1415, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 991, in stream_convert_to_parquet
                  builder._prepare_split(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1741, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1872, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
              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 17138 new columns ({'AP3B2', 'RP11-96L14.7', 'SMARCA4', 'NAA20', 'ZNF117', 'CCM2L', 'TBCC', 'KCNMB2-AS1', 'ACSM6', 'HAS3', 'TWF2', 'ZDHHC19', 'CACNA1C', 'YWHAE', 'CLN6', 'CCDC57', 'TAS2R5', 'PFDN2', 'SHANK2', 'GATA6', 'RACK1', 'IPMK', 'KIF5C', 'IGFBP2', 'RHOT2', 'THAP12', 'SERPINI2', 'ZNF229', 'MAPKAPK2', 'RFTN1', 'ARL9', 'GAPT', 'TAS2R20', 'FAM49B', 'PEX16', 'MYLIP', 'CYP2D6', 'ITM2C', 'ATP5J2', 'OR2A1-AS1', 'CXorf56', 'SLX1B', 'MRPL13', 'HP1BP3', 'TMEM115', 'PHB2', 'TRPV2', 'FAAP24', 'LCE6A', 'MAPK8IP2', 'SERPINB1', 'C5orf45', 'CTD-2007L18.5', 'TRIAP1', 'EXO1', 'REEP2', 'MSRB3', 'TMEM52', 'MRPL39', 'FAM156A', 'TRIM44', 'ZNF558', 'IDE', 'MATR3', 'ALDH16A1', 'SORBS3', 'ATPAF1', 'TGFBI', 'CPAMD8', 'IL15', 'CLHC1', 'CLEC12B', 'LRP11', 'SLC52A2', 'RP11-226E21.4', 'ZNF784', 'TMBIM6', 'SPERT', 'VIP', 'C2CD2', 'VGLL4', 'BMX', 'PPP1R3B', 'HNRNPH2', 'DSC2', 'BZW2', 'INPPL1', 'NPIPB11', 'RP11-679C8.2', 'ATP6V1A', 'CCDC120', 'KRT13', 'TBC1D1', 'LINGO2', 'PPP1R15B', 'UBA5', 'TMEM233', 'LRIF1', 'FAM131C', 'COIL', 'CRISPLD2', 'S100A8', 'PPEF1', 'ZNHIT3', 'TTYH1', 'FAM60A', 'H1FX', 'SGIP1', 'TM4SF18', 'ALKBH5', 'BEND6', 'PHB', 'STIM1', 'JUNB', 'IL32', 'LY6D', 'LINC01181', 'RPL41', 'TMED3', 'RGPD1', 'RP11-223P11.3', 'ATP12A', 'ALDH1A1', 'CDK5RAP1', 'TACC3', 'CIAPIN1', 'ASGR1', 'PLA2G4B', 'MREG', 'DUSP3', 'DUSP16', 'MIR1199', 'GALNT3', 'CCR5', 'SLC25A29', 'C7orf55', 'NCAPG', 'LIPE-AS1', 'SDF2', 'MSL2', 'TBC1D8', 'TREML1', 'ADHFE1', 'CHRDL1', 'CCND1', 'IL36G', 'C14orf166', 'SFTPD-AS1', 'PSMB7', 'CCS', 'KRT18', 
              ...
              ', 'PNPLA5', 'NUDT19', 'SRR', 'NPTXR', 'USP20', 'ADAM15', 'COX5B', 'PSENEN', 'HOXC4', 'ATAD5', 'C1orf228', 'STRA6', 'GMIP', 'RP1-71H19.2', 'TMEM184A', 'ZNF837', 'CCDC171', 'ASUN', 'TMEM59L', 'ERGIC3', 'DNAJB5', 'SLCO3A1', 'APITD1', 'RASA4', 'KIDINS220', 'ORAI3', 'FCRL1', 'HABP4', 'LA16c-385E7.1', 'HOXD3', 'PSMD6', 'PCDHGC3', 'NXT1', 'RBM43', 'DNASE1', 'LPAR1', 'VMO1', 'ACADVL', 'POLR3A', 'DEFB106A', 'MRVI1', 'CDK6', 'QTRT1', 'AP3S2', 'EFCAB10', 'TXNDC8', 'ZC3H13', 'AGPAT3', 'CDH18', 'PSMD11', 'SON', 'PLCL2', 'OBSL1', 'IL1RL2', 'PLA2G4A', 'RP11-2C24.9', 'SYT10', 'SMAD6', 'RP11-342C20.2', 'LDHB', 'CCDC81', 'KPTN', 'GEMIN7', 'NUDCD1', 'ANKRD23', 'NEMF', 'GATSL2', 'TRIM8', 'UHRF1', 'CLIC6', 'RCOR3', 'MYCL', 'SPACA6', 'DSEL', 'TCF3', 'EGR3', 'CERCAM', 'TCTN2', 'NPEPPS', 'LINC00998', 'AHNAK2', 'ARIH2', 'EAPP', 'VWC2', 'ATP6V1E2', 'ALG9', 'ITPKC', 'FAM188B', 'STX1A', 'KALRN', 'TMEM40', 'TNFAIP8L2', 'KIF11', 'RP11-982M15.2', 'LMAN2L', 'CTC-518B2.12', 'CORO2A', 'CCDC170', 'CASP7', 'TNPO1', 'CA5B', 'GALNT14', 'PROCA1', 'PCDHB4', 'PUSL1', 'PLAC1', 'ZNF680', 'DOCK1', 'ZDHHC15', 'LRRC39', 'RXFP1', 'AMOTL1', 'GOLGA6L4', 'RRBP1', 'KDM4C', 'CHMP6', 'RP11-368I7.4', 'ALPK3', 'IRAK4', 'PEBP1', 'ACTR2', 'RPRD1B', 'RP3-402G11.26', 'UNC5A', 'CYB561D1', 'AC104024.1', 'LIMS3', 'TLE2', 'TRIM26', 'KIAA1551', 'AIG1', 'DUSP8', 'PPP2R2D', 'USP36', 'KCNIP4', 'MID2', 'HIST1H1E', 'ARHGAP40', 'NAA15', 'DDX58', 'CAPN1', 'CAMK2B', 'FAM188A', 'SIN3B', 'TMED5', 'PRR26', 'OGFOD1', 'BEX3', 'CAPG', 'TPCN1', 'RPA2'}) and 3 missing columns ({'yaxis', 'xaxis', 'r'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/jiawennnn/STimage-1K4M/ST/gene_exp/GSE144239_GSM4284316_count.csv (at revision 1c2a89874eed9bb70606373d2b7551c9583a0131)
              
              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)

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Unnamed: 0
string
yaxis
float64
xaxis
float64
r
float64
GSE144239_GSM4284316_10x26
5,741.5
3,845.3
45.125581
GSE144239_GSM4284316_10x28
6,142.9
3,841.4
45.125581
GSE144239_GSM4284316_10x30
6,549.5
3,834.4
45.125581
GSE144239_GSM4284316_10x32
6,951.6
3,839.6
45.125581
GSE144239_GSM4284316_10x34
7,355.5
3,839.4
45.125581
GSE144239_GSM4284316_10x36
7,756.1
3,839.3
45.125581
GSE144239_GSM4284316_10x38
8,144.4
3,838.8
45.125581
GSE144239_GSM4284316_10x40
8,554.1
3,833.4
45.125581
GSE144239_GSM4284316_10x44
9,356.4
3,830.9
45.125581
GSE144239_GSM4284316_10x46
9,758
3,828.8
45.125581
GSE144239_GSM4284316_10x48
10,156
3,830.9
45.125581
GSE144239_GSM4284316_11x25
5,551.5
4,022.2
45.125581
GSE144239_GSM4284316_11x27
5,940.9
4,020.2
45.125581
GSE144239_GSM4284316_11x29
6,353
4,009.4
45.125581
GSE144239_GSM4284316_11x31
6,757.6
4,014.4
45.125581
GSE144239_GSM4284316_11x33
7,155.4
4,013.1
45.125581
GSE144239_GSM4284316_11x35
7,557.4
4,014.1
45.125581
GSE144239_GSM4284316_11x37
7,947.4
4,004.7
45.125581
GSE144239_GSM4284316_11x39
8,337.8
4,010.5
45.125581
GSE144239_GSM4284316_11x41
8,760.5
4,011.8
45.125581
GSE144239_GSM4284316_11x43
9,164.1
4,015.6
45.125581
GSE144239_GSM4284316_11x45
9,564
4,006.9
45.125581
GSE144239_GSM4284316_11x47
9,959.5
4,018.4
45.125581
GSE144239_GSM4284316_11x49
10,355.8
4,014.1
45.125581
GSE144239_GSM4284316_12x22
4,940.1
4,194.9
45.125581
GSE144239_GSM4284316_12x24
5,340.2
4,194.8
45.125581
GSE144239_GSM4284316_12x26
5,747.8
4,194.1
45.125581
GSE144239_GSM4284316_12x28
6,143.3
4,195.9
45.125581
GSE144239_GSM4284316_12x30
6,554.3
4,190.9
45.125581
GSE144239_GSM4284316_12x32
6,951.6
4,195.8
45.125581
GSE144239_GSM4284316_12x34
7,354.3
4,197.5
45.125581
GSE144239_GSM4284316_12x36
7,750.3
4,200.9
45.125581
GSE144239_GSM4284316_12x38
8,142.6
4,186.9
45.125581
GSE144239_GSM4284316_12x40
8,553.2
4,187.2
45.125581
GSE144239_GSM4284316_12x42
8,954.5
4,190.6
45.125581
GSE144239_GSM4284316_12x44
9,357.6
4,191.9
45.125581
GSE144239_GSM4284316_12x46
9,757.8
4,194.4
45.125581
GSE144239_GSM4284316_12x48
10,154.5
4,193.3
45.125581
GSE144239_GSM4284316_13x21
4,734.1
4,378
45.125581
GSE144239_GSM4284316_13x23
5,143
4,373.2
45.125581
GSE144239_GSM4284316_13x25
5,539.8
4,382.1
45.125581
GSE144239_GSM4284316_13x27
5,933.8
4,384.9
45.125581
GSE144239_GSM4284316_13x29
6,348.2
4,374.1
45.125581
GSE144239_GSM4284316_13x31
6,745.5
4,377.5
45.125581
GSE144239_GSM4284316_13x33
7,148.5
4,380.3
45.125581
GSE144239_GSM4284316_13x35
7,555.3
4,379
45.125581
GSE144239_GSM4284316_13x37
7,949.6
4,375.2
45.125581
GSE144239_GSM4284316_13x39
8,347.3
4,372.9
45.125581
GSE144239_GSM4284316_13x41
8,752.6
4,376.6
45.125581
GSE144239_GSM4284316_13x43
9,160.5
4,375.2
45.125581
GSE144239_GSM4284316_13x45
9,558.7
4,368.6
45.125581
GSE144239_GSM4284316_13x47
9,955.3
4,374.2
45.125581
GSE144239_GSM4284316_13x49
10,358.7
4,382.5
45.125581
GSE144239_GSM4284316_14x18
4,130.1
4,567
45.125581
GSE144239_GSM4284316_14x20
4,522.4
4,558.1
45.125581
GSE144239_GSM4284316_14x22
4,925.8
4,555.8
45.125581
GSE144239_GSM4284316_14x24
5,326.6
4,555.5
45.125581
GSE144239_GSM4284316_14x26
5,727
4,560.2
45.125581
GSE144239_GSM4284316_14x28
6,132.8
4,554.1
45.125581
GSE144239_GSM4284316_14x30
6,524.2
4,550.7
45.125581
GSE144239_GSM4284316_14x32
6,928.3
4,554.7
45.125581
GSE144239_GSM4284316_14x34
7,329
4,559.4
45.125581
GSE144239_GSM4284316_14x36
7,729.1
4,558.3
45.125581
GSE144239_GSM4284316_14x38
8,128.4
4,552.6
45.125581
GSE144239_GSM4284316_14x40
8,527.1
4,555.9
45.125581
GSE144239_GSM4284316_14x42
8,929.7
4,557.5
45.125581
GSE144239_GSM4284316_14x44
9,328.8
4,559.7
45.125581
GSE144239_GSM4284316_14x46
9,731.5
4,549.9
45.125581
GSE144239_GSM4284316_14x48
10,129.5
4,554.9
45.125581
GSE144239_GSM4284316_14x50
10,531.1
4,556.3
45.125581
GSE144239_GSM4284316_15x17
3,939.2
4,743.3
45.125581
GSE144239_GSM4284316_15x19
4,327.9
4,745.6
45.125581
GSE144239_GSM4284316_15x21
4,726.3
4,734.8
45.125581
GSE144239_GSM4284316_15x23
5,128.5
4,735.4
45.125581
GSE144239_GSM4284316_15x25
5,536.5
4,736.6
45.125581
GSE144239_GSM4284316_15x27
5,931.5
4,741.7
45.125581
GSE144239_GSM4284316_15x29
6,329.8
4,730
45.125581
GSE144239_GSM4284316_15x31
6,729.5
4,734.1
45.125581
GSE144239_GSM4284316_15x33
7,130.9
4,738.7
45.125581
GSE144239_GSM4284316_15x35
7,532.7
4,739.5
45.125581
GSE144239_GSM4284316_15x37
7,931.4
4,729.9
45.125581
GSE144239_GSM4284316_15x39
8,322
4,738.1
45.125581
GSE144239_GSM4284316_15x41
8,731
4,736.8
45.125581
GSE144239_GSM4284316_15x43
9,131.5
4,740
45.125581
GSE144239_GSM4284316_15x45
9,533.9
4,733.1
45.125581
GSE144239_GSM4284316_15x47
9,933.6
4,733.6
45.125581
GSE144239_GSM4284316_15x49
10,329.9
4,735.9
45.125581
GSE144239_GSM4284316_15x51
10,734.1
4,738.6
45.125581
GSE144239_GSM4284316_16x16
3,732.4
4,919.1
45.125581
GSE144239_GSM4284316_16x18
4,132.2
4,926.6
45.125581
GSE144239_GSM4284316_16x20
4,527.4
4,922.8
45.125581
GSE144239_GSM4284316_16x22
4,925.8
4,917.7
45.125581
GSE144239_GSM4284316_16x24
5,333.2
4,915.9
45.125581
GSE144239_GSM4284316_16x26
5,724.5
4,925.1
45.125581
GSE144239_GSM4284316_16x28
6,132.7
4,914
45.125581
GSE144239_GSM4284316_16x30
6,527.9
4,915.3
45.125581
GSE144239_GSM4284316_16x32
6,930.5
4,918.4
45.125581
GSE144239_GSM4284316_16x34
7,330
4,917.3
45.125581
GSE144239_GSM4284316_16x36
7,733
4,916.8
45.125581
GSE144239_GSM4284316_16x38
8,127.2
4,913
45.125581
End of preview.

STimage-1K4M Dataset

Welcome to the STimage-1K4M Dataset repository. This dataset is designed to foster research in the field of spatial transcriptomics, combining high-resolution histopathology images with detailed gene expression data.

teaser

Update

Feb 12, 2025 We corrected a typo in meta file (changed "Human_Brain+Kidney_10X_02212023_Visium" to "Mouse_Brain+Kidney_10X_02212023_Visium"). Please refer to meta_all_gene02122025.csv for the newest meta data.

Dataset Description

STimage-1K4M consists of 1,149 spatial transcriptomics slides, totaling over 4 million spots with paired gene expression data. This dataset includes:

  • Images.
  • Gene expression profiles matched with high-resolution histopathology images.
  • Spatial coordinates for each spot.

Data structure

The data structure is organized as follows:

β”œβ”€β”€ annotation              # Pathologist annotation
β”œβ”€β”€ meta                    # Test files (alternatively `spec` or `tests`)
β”‚   β”œβ”€β”€ bib.txt             # the bibtex for all studies with pmid included in the dataset
β”‚   β”œβ”€β”€ meta_all_gene.csv   # The meta information
β”œβ”€β”€ ST                      # Include all data for tech: Spatial Transcriptomics
β”‚   β”œβ”€β”€ coord               # Include the spot coordinates & spot radius of each slide
β”‚   β”œβ”€β”€ gene_exp            # Include the gene expression of each slide
β”‚   └── image               # Include the image each slide
β”œβ”€β”€ Visium                  # Include all data for tech: Visium, same structure as ST
β”œβ”€β”€ VisiumHD                # Include all data for tech: VisiumHD, same structure as ST

Repository structure

The code for data processing and reproducing evaluation result in the paper are in Document.

Acknowledgement

The fine-tuning and evaluation codes borrows heavily from CLIP and PLIP.

Citation

@misc{chen2024stimage1k4m,
      title={STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics}, 
      author={Jiawen Chen and Muqing Zhou and Wenrong Wu and Jinwei Zhang and Yun Li and Didong Li},
      year={2024},
      eprint={2406.06393},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}

License

All code is licensed under the MIT License - see the LICENSE.md file for details.

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