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Datasets:
jiawennnn
/
STimage-1K4M

Tasks:
Image Feature Extraction
Image Segmentation
Image Classification
Modalities:
Image
Languages:
English
Size:
100B<n<1T
ArXiv:
Tags:
biology
License:
Dataset card Viewer Files Community
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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 ({'RP3-382I10.7', 'MIR3180-4', 'IL4I1', 'ARL14EP', 'CDX2', 'GNA11', 'PDDC1', 'BRD2', 'PIGN', 'KIF1C', 'LRRC41', 'RP11-336A10.4', 'RP11-727F15.14', 'GNA13', 'TNPO1', 'TANK', 'ZCCHC2', 'LDOC1', 'PGS1', 'LINGO1', 'CCNK', 'ENTPD6', 'HESX1', 'DOCK11', 'CWC25', 'GJC2', 'NNAT', 'NDUFA6', 'SEMA4A', 'C2CD3', 'RAPGEFL1', 'SHF', 'POLR2E', 'DHRS7', 'EFNA5', 'MBOAT7', 'TMEM88', 'GOLPH3', 'CHID1', 'PPP2R5E', 'CCNB1IP1', 'CH507-24F1.2', 'GLT1D1', 'CARD16', 'ACER1', 'HSPA6', 'HSCB', 'ZBTB7C', 'MAGEH1', 'SCARA3', 'RFX1', 'UAP1L1', 'TTC7A', 'STAT5B', 'RAN', 'PARP3', 'HPSE', 'ANAPC16', 'AC006116.20', 'STYX', 'CLEC2B', 'KLF4', 'HCG18', 'TNFAIP1', 'QSOX2', 'GALNT6', 'RP11-442H21.2', 'HOXD1', 'GABBR2', 'LINC01621', 'ELL', 'CD48', 'CCDC81', 'SAE1', 'HS3ST6', 'CCSER2', 'UBE2J2', 'FOXB1', 'GJA3', 'TRIM68', 'RING1', 'C8orf44', 'EFCAB2', 'APAF1', 'AIFM1', 'CCT4', 'KLHL31', 'RPL32', 'LY9', 'C5orf45', 'CA2', 'RP11-30J20.1', 'SPATC1L', 'DLX5', 'RP11-532F12.5', 'B4GALT1', 'SPRYD4', 'FYTTD1', 'HEATR5B', 'LINC00441', 'HIST1H2AE', 'PSMB7', 'WDR6', 'CUTC', 'ERCC2', 'C16orf86', 'FAM72A', 'CSPG5', 'MCU', 'FZD6', 'SYK', 'TPGS2', 'PPT1', 'NPPC', 'HIBADH', 'C1orf116', 'GCC1', 'ENO4', 'PCMT1', 'EXD3', 'RNF103', 'TDRD12', 'SYT15', 'GGTLC3', 'FAM228A', 'KLC2', 'FUT1', 'CBSL', 'NRROS', 'TMEM156', 'ZNF720', 'RAB14', 'COQ9', 'AC092580.4', 'SCOC', 'SRP72', 'PIAS2', 'CUTA', 'NBAS', 'BMX', 'SLFN5', 'TRAF2', 'YBX2', 'ASIC1', 'SASS6', 'PRELP', 'ERP27', 'FBXL22', 'FBXO39', 'LTK', 'PDE6D', 'NOSTRIN', 'SYCP2', 'ZNF333', 'CSF2', '
...
7', 'NOP58', 'CKS1B', 'KDM7A', 'SOCS7', 'KATNAL2', 'RP11-66B24.2', 'CRACR2B', 'ABRACL', 'RPL31', 'TIMM10', 'CARMN', 'OR51E1', 'SPRYD3', 'GNB1L', 'NDC80', 'F2RL2', 'CDK20', 'PIK3C2B', 'HMG20A', 'CEACAM5', 'RAB32', 'METRNL', 'MYCBP2', 'INTS6-AS1', 'RGCC', 'IZUMO1', 'KEL', 'TM9SF1', 'PRR15', 'MMP25', 'PRR5', 'GLUD2', 'TMEM106A', 'VAMP1', 'DNAJC14', 'RNF122', 'NHSL1', 'RBCK1', 'EGLN1', 'CSRNP1', 'HSFX1', 'MED29', 'EPN3', 'MIEF1', 'GBA2', 'GZMM', 'NLRP2B', 'TIMM21', 'ATP11B', 'BBS2', 'PLPP7', 'PRKCQ', 'RP11-618L22.1', 'GSAP', 'STK38L', 'GS1-393G12.13', 'AC093388.3', 'B3GALT5', 'MEGF6', 'MUC15', 'CTD-2298J14.2', 'TRIM23', 'H2AFV', 'CA8', 'ATE1', 'FADD', 'BIN3', 'MPZ', 'MICAL2', 'FILIP1L', 'ZNF420', 'NME8', 'TPO', 'S100A12', 'TRIM37', 'AREG', 'WBSCR17', 'VSIG10L', 'ATG2B', 'MARCH9', 'PHEX', 'GTF2A2', 'RPS6KA5', 'IDI1', 'HSPA4', 'CDA', 'ASB12', 'STAU1', 'ZSCAN32', 'NDE1', 'C2CD2', 'ZNF83', 'INTS5', 'EMC7', 'DNAH2', 'EHD3', 'EMG1', 'TIPARP-AS1', 'VAMP7', 'CTC-260F20.3', 'MOSPD3', 'PELI2', 'FBXL17', 'UBR2', 'KCNN1', 'ANKRD54', 'PCGF3', 'ABR', 'ST3GAL1', 'CTB-12A17.3', 'ATP6AP2', 'RAB20', 'COX16', 'GTF2I', 'LMCD1', 'PANX1', 'ADAMDEC1', 'IKBIP', 'MYBPC3', 'TUBA1B', 'PPIAL4E', 'RGL4', 'NPIPB4', 'SERTAD1', 'FRYL', 'KCNK2', 'RAP1GAP', 'HOMER2', 'TMEM27', 'NME3', 'C15orf48', 'LPIN1', 'C1orf131', 'ARL6IP4', 'NDP', 'ZFAS1', 'TNC', 'H3F3B', 'ZNF205', 'C1QL1', 'SUSD4', 'FAM3A', 'LRRC66', 'C7orf55', 'C15orf41', 'CCDC78', 'IL6R', 'MAEA', 'COX6B1', 'EFCAB10', 'PHYHIP', 'KDM4C', 'PPP1R2P3', 'HELZ2'}) and 3 missing columns ({'xaxis', 'yaxis', '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 eb59a849e82d5e0f3bdd2fd269891dffd63da998)

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 2013, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, 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 2302, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, 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 1524, 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 1099, in stream_convert_to_parquet
                  builder._prepare_split(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1884, 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 2015, 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 ({'RP3-382I10.7', 'MIR3180-4', 'IL4I1', 'ARL14EP', 'CDX2', 'GNA11', 'PDDC1', 'BRD2', 'PIGN', 'KIF1C', 'LRRC41', 'RP11-336A10.4', 'RP11-727F15.14', 'GNA13', 'TNPO1', 'TANK', 'ZCCHC2', 'LDOC1', 'PGS1', 'LINGO1', 'CCNK', 'ENTPD6', 'HESX1', 'DOCK11', 'CWC25', 'GJC2', 'NNAT', 'NDUFA6', 'SEMA4A', 'C2CD3', 'RAPGEFL1', 'SHF', 'POLR2E', 'DHRS7', 'EFNA5', 'MBOAT7', 'TMEM88', 'GOLPH3', 'CHID1', 'PPP2R5E', 'CCNB1IP1', 'CH507-24F1.2', 'GLT1D1', 'CARD16', 'ACER1', 'HSPA6', 'HSCB', 'ZBTB7C', 'MAGEH1', 'SCARA3', 'RFX1', 'UAP1L1', 'TTC7A', 'STAT5B', 'RAN', 'PARP3', 'HPSE', 'ANAPC16', 'AC006116.20', 'STYX', 'CLEC2B', 'KLF4', 'HCG18', 'TNFAIP1', 'QSOX2', 'GALNT6', 'RP11-442H21.2', 'HOXD1', 'GABBR2', 'LINC01621', 'ELL', 'CD48', 'CCDC81', 'SAE1', 'HS3ST6', 'CCSER2', 'UBE2J2', 'FOXB1', 'GJA3', 'TRIM68', 'RING1', 'C8orf44', 'EFCAB2', 'APAF1', 'AIFM1', 'CCT4', 'KLHL31', 'RPL32', 'LY9', 'C5orf45', 'CA2', 'RP11-30J20.1', 'SPATC1L', 'DLX5', 'RP11-532F12.5', 'B4GALT1', 'SPRYD4', 'FYTTD1', 'HEATR5B', 'LINC00441', 'HIST1H2AE', 'PSMB7', 'WDR6', 'CUTC', 'ERCC2', 'C16orf86', 'FAM72A', 'CSPG5', 'MCU', 'FZD6', 'SYK', 'TPGS2', 'PPT1', 'NPPC', 'HIBADH', 'C1orf116', 'GCC1', 'ENO4', 'PCMT1', 'EXD3', 'RNF103', 'TDRD12', 'SYT15', 'GGTLC3', 'FAM228A', 'KLC2', 'FUT1', 'CBSL', 'NRROS', 'TMEM156', 'ZNF720', 'RAB14', 'COQ9', 'AC092580.4', 'SCOC', 'SRP72', 'PIAS2', 'CUTA', 'NBAS', 'BMX', 'SLFN5', 'TRAF2', 'YBX2', 'ASIC1', 'SASS6', 'PRELP', 'ERP27', 'FBXL22', 'FBXO39', 'LTK', 'PDE6D', 'NOSTRIN', 'SYCP2', 'ZNF333', 'CSF2', '
              ...
              7', 'NOP58', 'CKS1B', 'KDM7A', 'SOCS7', 'KATNAL2', 'RP11-66B24.2', 'CRACR2B', 'ABRACL', 'RPL31', 'TIMM10', 'CARMN', 'OR51E1', 'SPRYD3', 'GNB1L', 'NDC80', 'F2RL2', 'CDK20', 'PIK3C2B', 'HMG20A', 'CEACAM5', 'RAB32', 'METRNL', 'MYCBP2', 'INTS6-AS1', 'RGCC', 'IZUMO1', 'KEL', 'TM9SF1', 'PRR15', 'MMP25', 'PRR5', 'GLUD2', 'TMEM106A', 'VAMP1', 'DNAJC14', 'RNF122', 'NHSL1', 'RBCK1', 'EGLN1', 'CSRNP1', 'HSFX1', 'MED29', 'EPN3', 'MIEF1', 'GBA2', 'GZMM', 'NLRP2B', 'TIMM21', 'ATP11B', 'BBS2', 'PLPP7', 'PRKCQ', 'RP11-618L22.1', 'GSAP', 'STK38L', 'GS1-393G12.13', 'AC093388.3', 'B3GALT5', 'MEGF6', 'MUC15', 'CTD-2298J14.2', 'TRIM23', 'H2AFV', 'CA8', 'ATE1', 'FADD', 'BIN3', 'MPZ', 'MICAL2', 'FILIP1L', 'ZNF420', 'NME8', 'TPO', 'S100A12', 'TRIM37', 'AREG', 'WBSCR17', 'VSIG10L', 'ATG2B', 'MARCH9', 'PHEX', 'GTF2A2', 'RPS6KA5', 'IDI1', 'HSPA4', 'CDA', 'ASB12', 'STAU1', 'ZSCAN32', 'NDE1', 'C2CD2', 'ZNF83', 'INTS5', 'EMC7', 'DNAH2', 'EHD3', 'EMG1', 'TIPARP-AS1', 'VAMP7', 'CTC-260F20.3', 'MOSPD3', 'PELI2', 'FBXL17', 'UBR2', 'KCNN1', 'ANKRD54', 'PCGF3', 'ABR', 'ST3GAL1', 'CTB-12A17.3', 'ATP6AP2', 'RAB20', 'COX16', 'GTF2I', 'LMCD1', 'PANX1', 'ADAMDEC1', 'IKBIP', 'MYBPC3', 'TUBA1B', 'PPIAL4E', 'RGL4', 'NPIPB4', 'SERTAD1', 'FRYL', 'KCNK2', 'RAP1GAP', 'HOMER2', 'TMEM27', 'NME3', 'C15orf48', 'LPIN1', 'C1orf131', 'ARL6IP4', 'NDP', 'ZFAS1', 'TNC', 'H3F3B', 'ZNF205', 'C1QL1', 'SUSD4', 'FAM3A', 'LRRC66', 'C7orf55', 'C15orf41', 'CCDC78', 'IL6R', 'MAEA', 'COX6B1', 'EFCAB10', 'PHYHIP', 'KDM4C', 'PPP1R2P3', 'HELZ2'}) and 3 missing columns ({'xaxis', 'yaxis', '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 eb59a849e82d5e0f3bdd2fd269891dffd63da998)
              
              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
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

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:

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