cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13306714
title: Standardized Framework and Quantitative Benchmarking: Nuclear Segmentation platforms for Multiplexed Immunofluorescence data in Translational Studies

description: Paired nuclear ground truth annotated binary masks and segmentation binary masks predicted from different segmentation platforms can be found in external.zip and inhouse.zip. internal.zip was used for development of the nuclear segmentation evaluation pipeline while external.zip hosts data that was/can be used for benchmarking of nuclear segmentation performance for multiplexed immunofluorescence workflows in translational studies. external.zip contains ground-truth annotated binary masks from another dataset in synapse (https://doi.org/10.7303/SYN27624812). README_DAPI.md contains information about where to locate the raw DAPI nuclear intensities used by the different segmentation platforms to predict nuclei.

The naming convention of the ROIs used is as follows: "Sample ID_ULHC" where ULHC refers to the coordinates of the upper-left hand corner pixel of the ROI within the whole sample field, delimited by an underscore ("_"). E.g. For ROI "Bph2_45174_14597_160_246": "Bph2_45174_14597" is the sample ID and (246,160) is the ULHC pixel.

 

Citing

Please cite these sources if you use this data



Sankaranarayanan, A., Khachaturov, G., Smythe, K.S. & Mittal, S. Quantitative benchmarking of nuclear segmentation algorithms in multiplexed immunofluorescence imaging for translational studies. Commun Biol 8, 836 (2025). https://doi.org/10.1038/s42003-025-08184-8

Sankaranarayanan, A., Khachaturov, G., Smythe, K. S. & Mittal, S. Standardized framework and quantitative benchmarking: nuclear segmentation platforms for multiplexed immunofluorescence data in translational studies. Zenodo (2024). https://doi.org/10.5281/zenodo.12775616
DOI: 10.15468/dl.kcvxby
title: Occurrence Download

description: A dataset containing 13304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Living Specimen, Specimen, Occurrence evidence)",
 "Continent is North America",
 "Country is Mexico",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Coordinate reprojected, Country invalid, Country derived from coordinates, Continent derived from coordinates, Presumed swapped coordinate)",
 "TaxonKey is Canidae"
 ]
}

 The dataset includes 13304 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009373-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3s574t
title: Occurrence Download

description: A dataset containing 4619 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Euphorbia esula L.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 4619 records from 186 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009374-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evu54q
title: Occurrence Download

description: A dataset containing 171 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Zygophyllum xanthoxylum (Bunge) Maxim."
 ]
}

 The dataset includes 171 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006485-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/h7e-209-bg0
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pks-txf-4qp
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dx6-736-4rb
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/49p-4cd-hgn
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g4z-www-vse
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d2r-gtp-9gk
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z3d-4nv-qx8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/26v-mqs-amc
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eqt-fb8-1e1
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rd3-cxk-x4f
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/szg-jnc-cf6
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hlm-avc-8bj
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/26g-zvw-cx2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sph-mxg-2g4
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qnw-9z6-x4w
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7bb-5l1-ekh
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wyb-5y6-gew
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jfs-yq6-cwt
title: Neoeponides coryelli (Palmer, 1945)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h3t-pmw-d96
title: Bulimina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vkp-ntd-5zw
title: Ostracoda Latreille, 1802

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l2w-971-c2h
title: Quinqueloculina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xx1-ckx-h9r
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/91s-8jj-bg3
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lnp-z2g-wy7
title: Pteroplatus gracilis Buquet, 1840

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0lx-h73-bsy
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/thl-q02-37d
title: Fungi

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h1m-1ml-3gc
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hf6-pk8-wtf
title: Bolivina d'Orbigny, 1839

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t6t-br8-lre
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4ry-y2l-sef
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s11-0w4-kbv
title: Globigerina

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dmq-8cr-bzs
title: Sus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l71-qyl-7mq
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7sy-m7v-3yn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s4g-cnp-j3r
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a4z-ava-q4f
title: Cibicides Montfort, 1808

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/br2-zw4-efj
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pq4-0zl-w93
title: Loxoconcha Sars, 1866

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/va7-r4l-5f2
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yet-lwf-vsf
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.15470161
title: Nanotechnology publications by funding agencies

description: ** Example used for the construction of the dataset. Once the whole datset is downloaded (in this case, the whole best 10th percentile in Nanotechnology from 2012 to 2024), one may extract a list of subsets. For instance, if one downloaded only those publications which have at least one author affiliated in Mainland China, such download might be called "CN". Such file in .csv format will have WOS - univocal identifiers. For instance: "WOS:000336235800014" as a string variable. This implies to separate WOS from rest of text. At this point one may simply merge datasets using the whole dataset comprising in our case 49061 observations (publications) - see below. It is worth noting that each subset may overlap others in such a way that a publication may have both US affiliated scholars and China Mainland one. Same applies to single funding agency, or any other added variable which is represented by single extractions. **

 

 

merge 1:1 wos  using "C:[...]\myfolder\CN.dta"

gen CN = 1 if _merge ==3

 

 

** Example of csv extraction report

// Filter Summary:

// Dataset: InCites Dataset

// Schema:  Web of Science

// Time Period:  [2012, 2024]

// Include Early Access documents:  true

// Document Type:  [Article]

// Funding Data Source:  All Sources

// Domestic/International Collaboration:  All

// Research Area:  [NANOSCIENCE & NANOTECHNOLOGY]

// Location:  [CHINA MAINLAND]

// Top % Documents:  10

 

// Exported date  Jul 9, 2024.

//InCites dataset updated  2024-06-28. Includes Web of Science content indexed through 2024-05-31.

 

** All subsets extracted around same day
DOI: 10.5281/zenodo.15470162
title: Nanotechnology publications by funding agencies

description: ** Example used for the construction of the dataset. Once the whole datset is downloaded (in this case, the whole best 10th percentile in Nanotechnology from 2012 to 2024), one may extract a list of subsets. For instance, if one downloaded only those publications which have at least one author affiliated in Mainland China, such download might be called "CN". Such file in .csv format will have WOS - univocal identifiers. For instance: "WOS:000336235800014" as a string variable. This implies to separate WOS from rest of text. At this point one may simply merge datasets using the whole dataset comprising in our case 49061 observations (publications) - see below. It is worth noting that each subset may overlap others in such a way that a publication may have both US affiliated scholars and China Mainland one. Same applies to single funding agency, or any other added variable which is represented by single extractions. **

 

 

merge 1:1 wos  using "C:[...]\myfolder\CN.dta"

gen CN = 1 if _merge ==3

 

 

** Example of csv extraction report

// Filter Summary:

// Dataset: InCites Dataset

// Schema:  Web of Science

// Time Period:  [2012, 2024]

// Include Early Access documents:  true

// Document Type:  [Article]

// Funding Data Source:  All Sources

// Domestic/International Collaboration:  All

// Research Area:  [NANOSCIENCE & NANOTECHNOLOGY]

// Location:  [CHINA MAINLAND]

// Top % Documents:  10

 

// Exported date  Jul 9, 2024.

//InCites dataset updated  2024-06-28. Includes Web of Science content indexed through 2024-05-31.

 

** All subsets extracted around same day
DOI: 10.15468/dl.z6cdvq
title: Occurrence Download

description: A dataset containing 1415 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (USA.41_1, USA.34_1, USA.11_1)",
 "TaxonKey is Lontra canadensis"
 ]
}

 The dataset includes 1415 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029385-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc110815965
title: Proto-Sinaitic Inscription 367

description: [Text Description:] Proto-Sinaitic Inscription ❧ [Text or Publication Number Note:] Sinai 367 ❧ [Excavation Description:] Discovered in 1930 in tumulus 150m south of Mine L ❧ [Medium:] Stone ❧ [Script Note:] Early Alphabetic ❧ [Physical Object Description:] Stone block with inscription in steliform panel measuring 26 x 14 cm
DOI: 10.15468/dl.hm4t3w
title: Occurrence Download

description: A dataset containing 5325 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "Country is United States of America",
 "TaxonKey is Pinus palustris"
 ]
}

 The dataset includes 5325 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029389-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.azs5rn
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-83.23332 -11.36083,-42.62496 -11.36083,-42.62496 17.07086,-83.23332 17.07086,-83.23332 -11.36083))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anguilla rostrata"
 ]
}

 The dataset includes 107 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029390-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc110815894
title: Proto-Sinaitic Inscription 375c

description: [Text Description:] Proto-Sinaitic Inscription ❧ [Text or Publication Number Note:] Sinai 375c ❧ [Excavation Description:] Discovered in 1935 in excavation of Mine M ❧ [Medium:] Stone ❧ [Script Note:] Early Alphabetic ❧ [Physical Object Description:] Stone slabe (stele?), 22 x 16 cm
DOI: 10.3886/e240198
title: HIFLD OPEN Incorporated Places (Civil)

description: USGS developed The National Map Gazetteer as the Federal and national standard (ANSI INCITS 446-2008) for geographic nomenclature based on the Geographic Names Information System (GNIS). The National Map Gazetteer contains information about physical and cultural geographic features, geographic areas, and locational entities that are generally recognizable and locatable by name (have achieved some landmark status) and are of interest to any level of government or to the public for any purpose that would lead to the representation of the feature in printed or electronic maps and/or geographic information systems. The dataset includes features of all types in the United States, its associated areas, and Antarctica, current and historical, but not including roads and highways. The dataset holds the federally recognized name of each feature and defines the feature location by state, county, USGS topographic map, and geographic coordinates. Other attributes include names or spellings other than the official name, feature classification, and historical and descriptive information. The dataset assigns a unique, permanent feature identifier, the Feature ID, as a standard Federal key for accessing, integrating, or reconciling feature data from multiple data sets. This dataset is a flat model, establishing no relationships between features, such as hierarchical, spatial, jurisdictional, organizational, administrative, or in any other manner. As an integral part of The National Map, the Gazetteer collects data from a broad program of partnerships with federal, state, and local government agencies and other authorized contributors. The Gazetteer provides data to all levels of government and to the public, as well as to numerous applications through a web query site, web map, feature and XML services, file download services, and customized files upon request. The National Map download client allows free downloads of public domain geographic names data by state in a pipe-delimited text format. For additional information on the GNIS, go to https://www.usgs.gov/tools/geographic-names-information-system-gnis. See https://apps.nationalmap.gov/help/ for assistance with The National Map viewer, download client, services, or metadata. Data Refreshed March, 2025
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025.
DOI: 10.25549/inscriptifact-ouc110819763
title: Persepolis Fortification Elamite Tablet 2267.101, Fort 2267.101

description: [Text Description:] Administrative text with seal ❧ [Text or Publication Number Note:] Fort 2267.101 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. Seal impression on right edge. ❧ [Physical Object Note:] Left side of tablet missing.
DOI: 10.3886/e240198v1
title: HIFLD OPEN Incorporated Places (Civil)

description: USGS developed The National Map Gazetteer as the Federal and national standard (ANSI INCITS 446-2008) for geographic nomenclature based on the Geographic Names Information System (GNIS). The National Map Gazetteer contains information about physical and cultural geographic features, geographic areas, and locational entities that are generally recognizable and locatable by name (have achieved some landmark status) and are of interest to any level of government or to the public for any purpose that would lead to the representation of the feature in printed or electronic maps and/or geographic information systems. The dataset includes features of all types in the United States, its associated areas, and Antarctica, current and historical, but not including roads and highways. The dataset holds the federally recognized name of each feature and defines the feature location by state, county, USGS topographic map, and geographic coordinates. Other attributes include names or spellings other than the official name, feature classification, and historical and descriptive information. The dataset assigns a unique, permanent feature identifier, the Feature ID, as a standard Federal key for accessing, integrating, or reconciling feature data from multiple data sets. This dataset is a flat model, establishing no relationships between features, such as hierarchical, spatial, jurisdictional, organizational, administrative, or in any other manner. As an integral part of The National Map, the Gazetteer collects data from a broad program of partnerships with federal, state, and local government agencies and other authorized contributors. The Gazetteer provides data to all levels of government and to the public, as well as to numerous applications through a web query site, web map, feature and XML services, file download services, and customized files upon request. The National Map download client allows free downloads of public domain geographic names data by state in a pipe-delimited text format. For additional information on the GNIS, go to https://www.usgs.gov/tools/geographic-names-information-system-gnis. See https://apps.nationalmap.gov/help/ for assistance with The National Map viewer, download client, services, or metadata. Data Refreshed March, 2025
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025.
DOI: 10.25549/inscriptifact-ouc110815947
title: Proto-Sinaitic Inscription 367

description: [Text Description:] Proto-Sinaitic Inscription ❧ [Text or Publication Number Note:] Sinai 367 ❧ [Excavation Description:] Discovered in 1930 in tumulus 150m south of Mine L ❧ [Medium:] Stone ❧ [Script Note:] Early Alphabetic ❧ [Physical Object Description:] Stone block with inscription in steliform panel measuring 26 x 14 cm
DOI: 10.25549/inscriptifact-ouc110819963
title: Persepolis Fortification Elamite Tablet 2272.101, Fort 2272.101

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 2272.101 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. ❧ [Physical Object Note:] Upper left, upper right and lower right corners broken off. Damage on obverse, reverse.
DOI: 10.25549/inscriptifact-ouc110819902
title: Persepolis Fortification Elamite Tablet 2272.101, Fort 2272.101

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 2272.101 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. ❧ [Physical Object Note:] Upper left, upper right and lower right corners broken off. Damage on obverse, reverse.
DOI: 10.25549/inscriptifact-ouc110819785
title: Persepolis Fortification Elamite Tablet 2267.101, Fort 2267.101

description: [Text Description:] Administrative text with seal ❧ [Text or Publication Number Note:] Fort 2267.101 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. Seal impression on right edge. ❧ [Physical Object Note:] Left side of tablet missing.
DOI: 10.7910/dvn/abxcey
title: Wright Casebook Edited; Docketed Case: 23,282