cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14912363
title: Annotated datasets for cell segmentation from the RNA2seg study

description: Annotations from the RNA2seg study

# Annotation

This folder contains the manual annotation along the corresponding staining and RNA positionof the different datasets used in the RNA2seg paper.the bounds.json indicate the coordiante of the crop in the original dataset.

the shape folders contain the annotation in a "geopandas shape" format to be integrated in a spataildata. Each segmentation shape can be load with :

```    import geopandas as gpd    gdf = gpd.read_file(path2save_shape_organ / "shape.shp")```

All datasets staining images and transcripts come from https://vizgen.com/data-release-program/ (MERSCOPE FFPE Human Immuno-Oncology Data Release) except the mouse ileum dataset that come from :Petukhov, V., Xu, R.J., Soldatov, R.A. et al.Cell segmentation in imaging-based spatial transcriptomics.Nat Biotechnol 40, 345–354 (2022). https://doi.org/10.1038/s41587-021-01044-w

contact : alice.blondel@minesparis.psl.eu, thomas.defard@minesparis.psl.eu

 

RNA2seg Code : https://github.com/fish-quant/rna2seg
DOI: 10.15468/dl.adc62f
title: Occurrence Download

description: A dataset containing 17617 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "GadmGid is NZL.3_1",
 "Geometry POLYGON((172.36076 -43.86876,172.4219 -43.85961,172.7141 -43.83554,172.71603 -43.81003,172.67992 -43.80185,172.6366 -43.78692,172.37809 -43.83265,172.36076 -43.86876))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 17617 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001810-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28407503
title: the data of umbrella review of c677t and a1298c

description: By screening out appropriate articles from the database, extracting basic information and finally evaluating them with various evaluation methods.
DOI: 10.6084/m9.figshare.28407503.v2
title: the data of umbrella review of c677t and a1298c

description: By screening out appropriate articles from the database, extracting basic information and finally evaluating them with various evaluation methods.
DOI: 10.6084/m9.figshare.28407503.v1
title: the data of umbrella review of c677t and a1298c

description: By screening out appropriate articles from the database, extracting basic information and finally evaluating them with various evaluation methods.
DOI: 10.15468/dl.gqd2ru
title: Occurrence Download

description: A dataset containing 255001 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arenaria serpyllifolia L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 255001 records from 1772 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001809-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccyyll1
title: CCDC 892384: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczqb55
title: CCDC 915187: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyylm2
title: CCDC 892385: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczqb66
title: CCDC 915188: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyyln3
title: CCDC 892386: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyylp4
title: CCDC 892387: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczqb77
title: CCDC 915189: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczqb88
title: CCDC 915190: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczqb99
title: CCDC 915191: Experimental Crystal Structure Determination

description: Related Article: Hsin-Yau Lin, Chih-Yuan Chin, Hui-Lin Huang, Wen-Yen Huang, Ming-Jhe Sie, Li-Hsun Huang, Yuan-Han Lee, Chia-Her Lin, Kwang-Hwa Lii, Xianhui Bu, Sue-Lein Wang|2013|Science|339|811|doi:10.1126/science.1232097
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczbvx1
title: CCDC 904174: Experimental Crystal Structure Determination

description: Related Article: Juan Xiao, Yuan Wu, Mian Li, Bao-Yu Liu, Xiao-Chun Huang, Dan Li|2013|Chem.-Eur.J.|19|1891|doi:10.1002/chem.201203515
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczbvy2
title: CCDC 904175: Experimental Crystal Structure Determination

description: Related Article: Juan Xiao, Yuan Wu, Mian Li, Bao-Yu Liu, Xiao-Chun Huang, Dan Li|2013|Chem.-Eur.J.|19|1891|doi:10.1002/chem.201203515
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczbvz3
title: CCDC 904176: Experimental Crystal Structure Determination

description: Related Article: Juan Xiao, Yuan Wu, Mian Li, Bao-Yu Liu, Xiao-Chun Huang, Dan Li|2013|Chem.-Eur.J.|19|1891|doi:10.1002/chem.201203515
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyx7hk
title: CCDC 891079: Experimental Crystal Structure Determination

description: Related Article: A.Sikorski, D.Trzybinski|2013|Tetrahedron Lett.|54|1463|doi:10.1016/j.tetlet.2013.01.026
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyx7jl
title: CCDC 891080: Experimental Crystal Structure Determination

description: Related Article: A.Sikorski, D.Trzybinski|2013|Tetrahedron Lett.|54|1463|doi:10.1016/j.tetlet.2013.01.026
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccspnps
title: CCDC 735806: Experimental Crystal Structure Determination

description: Related Article: S. Ivkovic, Violeta Jevtovic|2010|Journal of Engineering and Processing Management|2|7|
description: Related Article: Violeta Jevtovic|2014|American Journal of Chemistry|4|47|doi:10.5923/j.chemistry.20140401.08
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/x3s372
title: Données naturalistes opportunistes issues de la plateforme INaturalist-Données naturalistes opportunistes "nichard"

description: Données naturalistes opportunistes saisies sur iNaturalist à partir du compte "nichard"
DOI: 10.5517/ccz2056
title: CCDC 895657: Experimental Crystal Structure Determination

description: Related Article: N.Kadoya, M.Murai, M.Ishiguro, J.Uenishi, M.Uemura|2013|Tetrahedron Lett.|54|512|doi:10.1016/j.tetlet.2012.11.071
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccytt0k
title: CCDC 888739: Experimental Crystal Structure Determination

description: Related Article: L.Dobrzanska, E.Stander-Grobler, C.E.Strasser, S.Cronje, H.G.Raubenheimer|2012|Helv.Chim.Acta|95|2528|doi:10.1002/hlca.201200365
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccytt1l
title: CCDC 888740: Experimental Crystal Structure Determination

description: Related Article: L.Dobrzanska, E.Stander-Grobler, C.E.Strasser, S.Cronje, H.G.Raubenheimer|2012|Helv.Chim.Acta|95|2528|doi:10.1002/hlca.201200365
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccytt2m
title: CCDC 888741: Experimental Crystal Structure Determination

description: Related Article: L.Dobrzanska, E.Stander-Grobler, C.E.Strasser, S.Cronje, H.G.Raubenheimer|2012|Helv.Chim.Acta|95|2528|doi:10.1002/hlca.201200365
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccytt3n
title: CCDC 888742: Experimental Crystal Structure Determination

description: Related Article: L.Dobrzanska, E.Stander-Grobler, C.E.Strasser, S.Cronje, H.G.Raubenheimer|2012|Helv.Chim.Acta|95|2528|doi:10.1002/hlca.201200365
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccytt4p
title: CCDC 888743: Experimental Crystal Structure Determination

description: Related Article: L.Dobrzanska, E.Stander-Grobler, C.E.Strasser, S.Cronje, H.G.Raubenheimer|2012|Helv.Chim.Acta|95|2528|doi:10.1002/hlca.201200365
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccytt5q
title: CCDC 888744: Experimental Crystal Structure Determination

description: Related Article: L.Dobrzanska, E.Stander-Grobler, C.E.Strasser, S.Cronje, H.G.Raubenheimer|2012|Helv.Chim.Acta|95|2528|doi:10.1002/hlca.201200365
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyz445
title: CCDC 892897: Experimental Crystal Structure Determination

description: Related Article: A.I. Poddel'sky, I.V. Smolyaninov, N.T. Berberova, G.K. Fukin, V.K. Cherkasov, G.A. Abakumov|2015|J.Organomet.Chem.|789-790|8|doi:10.1016/j.jorganchem.2015.04.045
description: Related Article: G.K.Fukin, E.V.Baranov, A.I.Poddelskii, V.K.Cherkasov, G.A.Abakumov|2012|ChemPhysChem|13|3773|doi:10.1002/cphc.201200728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyz456
title: CCDC 892898: Experimental Crystal Structure Determination

description: Related Article: A.I. Poddel'sky, I.V. Smolyaninov, N.T. Berberova, G.K. Fukin, V.K. Cherkasov, G.A. Abakumov|2015|J.Organomet.Chem.|789-790|8|doi:10.1016/j.jorganchem.2015.04.045
description: Related Article: G.K.Fukin, E.V.Baranov, A.I.Poddelskii, V.K.Cherkasov, G.A.Abakumov|2012|ChemPhysChem|13|3773|doi:10.1002/cphc.201200728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccyz467
title: CCDC 892899: Experimental Crystal Structure Determination

description: Related Article: G.K.Fukin, E.V.Baranov, A.I.Poddelskii, V.K.Cherkasov, G.A.Abakumov|2012|ChemPhysChem|13|3773|doi:10.1002/cphc.201200728
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccsrk57
title: CCDC 737619: Experimental Crystal Structure Determination

description: Related Article: C.G.Cummings, A.D.Hamilton|2013|Tetrahedron|69|1663|doi:10.1016/j.tet.2012.11.070
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczcbl7
title: CCDC 904629: Experimental Crystal Structure Determination

description: Related Article: G.Markopoulos, L.Henneicke, J.Shen, Y.Okamoto, P.G.Jones, H.Hopf|2012|Angew.Chem.,Int.Ed.|51|12884|doi:10.1002/anie.201207220
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczcbm8
title: CCDC 904630: Experimental Crystal Structure Determination

description: Related Article: G.Markopoulos, L.Henneicke, J.Shen, Y.Okamoto, P.G.Jones, H.Hopf|2012|Angew.Chem.,Int.Ed.|51|12884|doi:10.1002/anie.201207220
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczcbn9
title: CCDC 904631: Experimental Crystal Structure Determination

description: Related Article: G.Markopoulos, L.Henneicke, J.Shen, Y.Okamoto, P.G.Jones, H.Hopf|2012|Angew.Chem.,Int.Ed.|51|12884|doi:10.1002/anie.201207220
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczcbpb
title: CCDC 904632: Experimental Crystal Structure Determination

description: Related Article: G.Markopoulos, L.Henneicke, J.Shen, Y.Okamoto, P.G.Jones, H.Hopf|2012|Angew.Chem.,Int.Ed.|51|12884|doi:10.1002/anie.201207220
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cczcbqc
title: CCDC 904633: Experimental Crystal Structure Determination

description: Related Article: G.Markopoulos, L.Henneicke, J.Shen, Y.Okamoto, P.G.Jones, H.Hopf|2012|Angew.Chem.,Int.Ed.|51|12884|doi:10.1002/anie.201207220
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.