cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.j5szgc
title: Occurrence Download

description: A dataset containing 27930 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pyrochroa coccinea (Linnaeus, 1761), Pyrola chlorantha Sw.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 27930 records from 358 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0325779-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pnez5d
title: Occurrence Download

description: A dataset containing 321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Muhlenbergia capillaris (Lam.) Trin.",
 "Year 1981-2010"
 ]
}

 The dataset includes 321 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0390984-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3djqg
title: Occurrence Download

description: A dataset containing 35520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 9869.0-1000000.0",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 35520 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000567-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qknz9
title: Occurrence Download

description: A dataset containing 4086 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.23.16_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset includes 4086 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0391074-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w7ykqv
title: Occurrence Download

description: A dataset containing 10709 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fraxinus Tourn. ex L.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (United States of America, Canada)"
 ]
}

 The dataset includes 10709 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0327750-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wra3gy
title: Occurrence Download

description: A dataset containing 17564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Bactrocera dorsalis (Hendel, 1912)"
 ]
}

 The dataset includes 17564 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0204092-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wjv627
title: Occurrence Download

description: A dataset containing 16109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "Continent is North America",
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lymantria dispar Linnaeus, 1758"
 ]
}

 The dataset includes 16109 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016092-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jut998
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is National Trust Species Records",
 "Month is May",
 "OccurrenceId is DSS000460000E13X",
 "Year 2012-2012"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0166092-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdqkhv
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aphyosemion christyi (Boulenger, 1915)"
 ]
}

 The dataset includes 145 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0325794-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ne6fra
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "DatasetKey is one of (Colección de Invertebrados Museo de La Salle Bogotá (MLS), Snow Entomological Museum Collection, Colección Entomológica de la Orinoquia (CEO), Bee Biology and Systematics Laboratory, Abejas (Hymenoptera: Apoidea: Anthophila) en un bosque seco tropical del Parque Natural Regional Los Besotes, Valledupar - Cesar, Colombia, Abejas (Hymenoptera: Apoidea: Apiformes) del Centro de Colecciones Biológicas de la Universidad del Magdalena (2006-2015), hymenoptera, Museo Entomológico Francisco Luis Gallego UNAL-MED, Evaluación de los insectos visitantes florales del café en Colombia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Xylocopa frontalis (Olivier, 1789)"
 ]
}

 The dataset includes 75 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002232-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpxshx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Magnoliopsida, Liliopsida)",
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Geometry MULTIPOLYGON (((132.788 61.346, 133.172 61.29421, 133.9973 61.49457, 133.8391 61.7716, 132.4597 61.91377, 132.1741 61.7245, 132.788 61.346)), ((132.7805 60.82168, 132.0968 60.92582, 131.9449 60.53315, 132.7805 60.82168)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0176665-210914110416597/datasets/export for details.
DOI: 10.15468/dl.hr9vu5
title: Occurrence Download

description: A dataset containing 5564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Botrychium Sw.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (United States of America, Canada)"
 ]
}

 The dataset includes 5564 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0327757-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kgtpt6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Didymascella chamaecyparidis (J.F.Adams) Maire",
 {
 "not" : {
 "Country" : [
 "is United States of America"
 ]
 }
 },
 {
 "not" : {
 "Country" : [
 "is Canada"
 ]
 }
 },
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109227-230530130749713/datasets/export for details.
DOI: 10.15468/dl.sbu3u9
title: Occurrence Download

description: A dataset containing 4333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Megascops asio (Linnaeus, 1758)",
 "HasCoordinate is True",
 "Country is United States of America",
 "Year is greater than or equal to 1999",
 "Year is less than or equal to 2001",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False",
 "DecimalLatitude is greater than or equal to 24.5",
 "DecimalLatitude is less than or equal to 49.5",
 "DecimalLongitude is greater than or equal to -125.0",
 "DecimalLongitude is less than or equal to -66.5"
 ]
}

 The dataset includes 4333 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0390847-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xpsz6s
title: Occurrence Download

description: A dataset containing 14358 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Philesturnus rufusater (R.P.Lesson, 1828)"
 ]
}

 The dataset includes 14358 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000571-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.578ryk
title: Occurrence Download

description: A dataset containing 537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-78.36182 -47.63916,-76.0669 -53.93799,-67.66113 -57.48535,-56.48682 -53.10791,-47.75208 -26.48499,-47.88117 -25.11597,-49.37653 -24.21051,-49.5221 -22.99378,-51.0846 -22.70081,-53.39173 -22.40784,-54.27063 -23.86047,-55.11963 -23.66455,-55.44068 -22.03735,-57.78443 -21.9397,-57.61353 -20.81665,-58.04932 -19.51416,-60.1001 -18.78174,-61.90003 -19.50256,-62.81372 -21.30493,-64.49829 -22.18384,-66.52466 -21.67114,-67.35474 -22.55005,-67.88147 -21.67542,-67.96692 -19.99085,-69.11255 -17.52075,-69.91455 -17.41455,-70.45166 -18.39111,-78.36182 -47.63916))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Xanthium L."
 ]
}

 The dataset includes 537 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0327760-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vepks9
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is China",
 "Country is Chinese Taipei",
 "Country is Macao",
 "Country is Hong Kong"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Bassia dasyphylla (Fisch. & C.A.Mey.) Kuntze"
 ]
}

 The dataset includes 159 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0267652-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rxg585
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dzihunia turdakovi Prokofiev, 2003"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0325800-210914110416597/datasets/export for details.
DOI: 10.15468/dl.jee46y
title: Occurrence Download

description: A dataset containing 836545 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 836545 records from 404 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000565-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11636384
title: Spheroid LSFM dataset with nuclei centroid annotations

description: Description

This repository contains 1) A dataset of lightsheet images of spheroids of two different cell lines (LN18-RED and SH-SY5Y) and centroid annotations for model training and evaluation; and 2) Weights of nuclei centroid prediction models trained on this data. See the pre-printreferenced below for more information.If you use this dataset or the models in your research, please cite our paper:





Van De Looverbosch, Tim, Sarah De Beuckeleer, Frederik De Smet, Jan Sijbers, and Winnok H. De Vos. “Proximity Adjusted Centroid Mapping for Accurate Detection of Nuclei in Dense 3D Cell Systems.” Computers in Biology and Medicine 185 (February 1, 2025): 109561. https://doi.org/10.1016/j.compbiomed.2024.109561.

The code accompanying our paper is available at https://github.com/DeVosLab/PAC-MAP. 



Dataset

Organization

The dataset is organized in the following way:



LN18-RED



pretrain (pretraining data with weak annotations)



patches



sample_01



patch_0000.tif

...



...



patches_binary (used to filter out patches with a lot of background)



sample_01



patch_0000.tif

...



...



points_csv (weak nuclei centroid annotations from seeded watershed)



sample_01



patch_0000.csv

...



...







SH-SY5Y



train (training/validation data with manual annotations)



patches



sample_XX



patch_xxxx.tif

...



...



points_csv



sample_XX



patch_xxxx.csv

...



...





test (test data with manual anntotations)



patches



sample_XX



patch_yyyy.tif

...



...



points_csv



sample_XX



patch_yyyy.csv

...



...







preprocessed_images (preprocessed in-toto images added for reference)



LN-18-RED



sample_01.tif

...



SH-SY5Y



sample_01.tif

...






Dataset generation

See the materials and methods in our pre-print.

Models

Pretrained, trained from scratch and finetuned models (C-MAP and PAC-MAP versions) for nuclei centroid prediction are provided for this LSFM spheroid dataset and for the LSFM mouse brain dataset provided by Krupa et al. (2021) (https://doi.org/10.1016/j.celrep.2021.109802). See our pre-print for usage, model training procedures and model performance. For each model type (pretrained, scratch, finetuned), model training was repeated three times with a different random seed (indicated in the model name).
DOI: 10.5281/zenodo.14138806
title: Spheroid LSFM dataset with nuclei centroid annotations

description: Description

This repository contains 1) A dataset of lightsheet images of spheroids of two different cell lines (LN18-RED and SH-SY5Y) and centroid annotations for model training and evaluation; and 2) Weights of nuclei centroid prediction models trained on this data. See the pre-printreferenced below for more information.If you use this dataset or the models in your research, please cite our paper:





Van De Looverbosch, Tim, Sarah De Beuckeleer, Frederik De Smet, Jan Sijbers, and Winnok H. De Vos. “Proximity Adjusted Centroid Mapping for Accurate Detection of Nuclei in Dense 3D Cell Systems.” Computers in Biology and Medicine 185 (February 1, 2025): 109561. https://doi.org/10.1016/j.compbiomed.2024.109561.

The code accompanying our paper is available at https://github.com/DeVosLab/PAC-MAP. 



Dataset

Organization

The dataset is organized in the following way:



LN18-RED



pretrain (pretraining data with weak annotations)



patches



sample_01



patch_0000.tif

...



...



patches_binary (used to filter out patches with a lot of background)



sample_01



patch_0000.tif

...



...



points_csv (weak nuclei centroid annotations from seeded watershed)



sample_01



patch_0000.csv

...



...







SH-SY5Y



train (training/validation data with manual annotations)



patches



sample_XX



patch_xxxx.tif

...



...



points_csv



sample_XX



patch_xxxx.csv

...



...





test (test data with manual anntotations)



patches



sample_XX



patch_yyyy.tif

...



...



points_csv



sample_XX



patch_yyyy.csv

...



...







preprocessed_images (preprocessed in-toto images added for reference)



LN-18-RED



sample_01.tif

...



SH-SY5Y



sample_01.tif

...






Dataset generation

See the materials and methods in our pre-print.

Models

Pretrained, trained from scratch and finetuned models (C-MAP and PAC-MAP versions) for nuclei centroid prediction are provided for this LSFM spheroid dataset and for the LSFM mouse brain dataset provided by Krupa et al. (2021) (https://doi.org/10.1016/j.celrep.2021.109802). See our pre-print for usage, model training procedures and model performance. For each model type (pretrained, scratch, finetuned), model training was repeated three times with a different random seed (indicated in the model name).
DOI: 10.15468/dl.t28eza
title: Occurrence Download

description: A dataset containing 7774 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Living Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sonchus asper (L.) Hill",
 "Year 1970-2025"
 ]
}

 The dataset includes 7774 records from 455 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005643-250117142028555/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.28245896
title: Prediction of Response to Immunotherapy based on scRNA-seq analysis

description: Immune checkpoint blockade (ICB) therapy has demonstrated remarkable treatment efficacy in a diverse range of cancers. However, it faces the challenge that only a small proportion of patients benefit from it. Using single-cell RNA-sequencing (scRNA-seq) data to predict patients' responses to ICB is a potential strategy for realizing precision medicine in ICB therapy.We set up an accessible pipeline for scRNA-seq data obtaining and analysis in the context of clinical use, and develop a tool named RedeTIL which can analyze single-cell features, including cell abundance and spatial topology of cells, to predict ICB-response. In order to demonstrate the predictive strength of scRNA-seq data, we obtained scRNA-seq data from 11 colorectal cancer (CRC) patients undergoing anti-PD-1 therapy according to our setted pipeline. Besides we collected publicly available scRNA-seq data of 39 breast cancer patients prior to receiving anti-PD-1 therapy, and data derived from 427 patients/samples across 15 tumor types for which objective response rates of anti-PD-1 or anti-PD-L1 were already reported. We used RedeTIL to extract these single-cell-derived features and then correlated them with clinical outcomes.Correlation analysis between single-cell based features and clinical outcomes shows the strong predictive strength of scRNA-seq data. For example, abundance of specific T cell subsets (e,g. CXCL13+ T and PDCD1+ T) has been found to correlate with shrinkage of CRC, and is more enriched in breast cancer responders compared to non-responders. Notably, the infiltration change metrics evaluated by RedeTIL have emerged as the most robust and accurate predictors. The spatial proximity of CD69+ T cells to cancer cells has been shown to correlate with shrinkage of CRC (Pearson R = 0.67, P = 0.02), and is also significantly enriched in Breast cancer responders than non-responders (P = 0.001), moreover, it has exhibited a high correlation with clinical objective response rate to Anti-PD-1/PD-L1 therapy across various cancer types (Pearson R = 0.8, P &lt; 0.001). Additionally, RedeTIL can be utilized to recommend mono- or combined drugs for individual patients.Our results proven that the application of scRNA-seq in predicting the response to immunotherapy in the clinical field is feasible, which can provide abundant and accurate information for treatment decisions, so as to achieve precision therapy.
DOI: 10.15468/dl.7bup8j
title: Occurrence Download

description: A dataset containing 276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "TaxonKey is Dasycrotapha speciosa Tweeddale, 1878"
 ]
}

 The dataset includes 276 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005645-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tphppx
title: Occurrence Download

description: A dataset containing 18765 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Living Specimen, Occurrence evidence, Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sorghum bicolor (L.) Moench",
 "Year 1970-2025"
 ]
}

 The dataset includes 18765 records from 303 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005646-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25958/e7jp-p396
title: EmbSCU
DOI: 10.15468/dl.s5t7sg
title: Occurrence Download

description: A dataset containing 47533242 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2015-2025"
 ]
}

 The dataset includes 47533242 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005584-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.