cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12656468
title: Cellpose training data and scripts from "Machine learning for histological annotation and quantification of cortical layers"

description: This Workflow contains all the material necessary to reproduce the cells detection, thanks to the QuPath performed in the paper

 "Machine learning for histological annotation and quantification of cortical layers"

Inside this workflow and dataset, you will find the following folders



QuPath Training Project: A QuPath 0.5.0 project containing all the manual annotations (ground truths) used to train the cellpose model, as well as the script to start the training

Training Images and Demo Images: The raw whole slide scanner images needed by the above QuPath project

Model: The fodler containing the trained cellpose model

cellpose-training Folder: The exported raw and ground truth images that the above cellpose model was trained on

Scripts: The QuPath scripts, also located in their respective QuPath projects, that were created for this whole workflow

QC: A Jupyter notebook, based on ZeroCostDL4Mic that computes quality metrics in order to assess the performance of the trained cellpose model. The folder also contains the resulting metrics.


Installation and Use

If you are going to use the QuPath projects, you need a local QuPath Installation https://qupath.github.io/ that is configured to run the QuPath Cellpose Extension https://github.com/BIOP/qupath-extension-cellpose as well as a working Cellpose installation https://github.com/MouseLand/cellpose

Instructions for installation are available from the links above.

After that, you should be able to open the QuPath project, navigate to the "Automate > Project scripts" menu and locate the script you wish to run.

1. train a cell segmentation algorithm in the context of the rat brain Layer Boundaries project 

2. trigger cell segmentation from a QuPath project in a semi-automated pipeline
DOI: 10.15468/dl.59canc
title: Occurrence Download

description: A dataset containing 2434 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Spiranthes sinensis (Pers.) Ames"
 ]
}

 The dataset includes 2434 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025564-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rujjb6
title: Occurrence Download

description: A dataset containing 12991 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Marine bird density and distribution on Canada's Pacific coast, 2005-2008"
 ]
}

 The dataset includes 12991 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025563-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fqjcbn
title: Occurrence Download

description: A dataset containing 372 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Instituto Boto Cinza Guiana dolphin distribution between 2005-2007 in Sepetiba Bay, Brazil"
 ]
}

 The dataset includes 372 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025566-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfbmnv
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Butumia marginalis G.Taylor"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025567-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11549998
title: Västerbotten & Norrbotten Counties (Sweden) - NEVERMORE Climate Dataset

description: The dataset consist of the historical and climate projection (CMIP6) for gridded atmospheric variables and the climate hazards/extreme events alongside the return values (likelihood) of hazards/extreme events. The dataset was developed during NEVERMORE project as part of WP3 from CMCC and NCSRD.
DOI: 10.5281/zenodo.11549999
title: Västerbotten & Norrbotten Counties (Sweden) - NEVERMORE Climate Dataset

description: The dataset consist of the historical and climate projection (CMIP6) for gridded atmospheric variables and the climate hazards/extreme events alongside the return values (likelihood) of hazards/extreme events. The dataset was developed during NEVERMORE project as part of WP3 from CMCC and NCSRD.
DOI: 10.5281/zenodo.14195683
title: Västerbotten & Norrbotten Counties (Sweden) - NEVERMORE Climate Dataset

description: The dataset consist of the historical and climate projection (CMIP6) for gridded atmospheric variables and the climate hazards/extreme events alongside the return values (likelihood) of hazards/extreme events. The dataset was developed during NEVERMORE project as part of WP3 from CMCC and NCSRD.
DOI: 10.15468/dl.vfykhp
title: Occurrence Download

description: A dataset containing 1142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mitridae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1142 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025568-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k38fyt
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicraeanthus africanus Engl."
 ]
}

 The dataset includes 128 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025569-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g2ffh7
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Butumia marginalis G.Taylor"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025571-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.csza62
title: Occurrence Download

description: A dataset containing 610 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Country is Spain",
 "DatasetKey is one of (FloraCAT: Banco de datos de los cormófitos de Cataluña, CSIC-Real Jardín Botánico-Anthos. Sistema de Información de las Plantas de España, Sistema de Información de la vegetación Ibérica y Macaronésica, CSIC-Real Jardín Botánico-Colección de Plantas Vasculares (MA), Banco de Datos de la Biodiversidad de la Comunitat Valenciana)",
 "Geometry POLYGON((0.69219 42.93125,0.21782 41.30852,0.5373 41.13376,0.3824 40.68013,0.9439 40.67278,0.83741 40.80482,1.19561 41.01699,2.26052 41.23576,2.36701 41.41751,3.2383 41.80114,3.36416 42.08917,3.36416 42.44022,2.90915 42.56156,2.54127 42.42593,0.69219 42.93125))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio lividus L."
 ]
}

 The dataset includes 610 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025570-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14195897
title: Finnish referative constructions and subordinate että clauses in the Bible translations 1548-2020, coded verses

description: Aineisto sisältää tiedot vuoden 1548 Uudesta testamentista haettujen referatiivirakenteiden ja että-lauseiden paikoista, jakaumasta ja matriisilauseiden verbeistä sekä vastineista uudemmissa raamatunkäännöksissä.

Lähteet:

Biblia. 1642. Biblia. Se on: coco pyhä Ramattu, suomexi. Stockholm: Henrich Keyser.

Biblia. 1776. Biblia. Se on: coco pyhä Ramattu, suomexi. Turku: Johan Christopher Frenckell.

Raamattu. 1938. Pyhä Raamattu. Sortavala: Suomen kirkon sisälähetysseura.

Raamattu. 1992. Pyhä Raamattu. Helsinki: Suomen Pipliaseura.

Se Wsi Testamenti = The Morpho-Syntactic Database of Mikael Agricola's Works version 1.1, Korp. The database is available through the Korp Interface at http://korp.csc.fi/. Access location: http://urn.fi/urn:nbn:fi:lb-2019121803.

 Uusi testamentti 2020 – Raamattu mobiilikäyttäjille. 2020. Helsinki: Suomen Pipliaseura.
DOI: 10.5281/zenodo.14195898
title: Finnish referative constructions and subordinate että clauses in the Bible translations 1548-2020, coded verses

description: Aineisto sisältää tiedot vuoden 1548 Uudesta testamentista haettujen referatiivirakenteiden ja että-lauseiden paikoista, jakaumasta ja matriisilauseiden verbeistä sekä vastineista uudemmissa raamatunkäännöksissä.

Lähteet:

Biblia. 1642. Biblia. Se on: coco pyhä Ramattu, suomexi. Stockholm: Henrich Keyser.

Biblia. 1776. Biblia. Se on: coco pyhä Ramattu, suomexi. Turku: Johan Christopher Frenckell.

Raamattu. 1938. Pyhä Raamattu. Sortavala: Suomen kirkon sisälähetysseura.

Raamattu. 1992. Pyhä Raamattu. Helsinki: Suomen Pipliaseura.

Se Wsi Testamenti = The Morpho-Syntactic Database of Mikael Agricola's Works version 1.1, Korp. The database is available through the Korp Interface at http://korp.csc.fi/. Access location: http://urn.fi/urn:nbn:fi:lb-2019121803.

 Uusi testamentti 2020 – Raamattu mobiilikäyttäjille. 2020. Helsinki: Suomen Pipliaseura.
DOI: 10.15468/dl.fn6czw
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Butumia marginalis G.Taylor"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025572-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6uup7q
title: Occurrence Download

description: A dataset containing 3212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Columbellidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3212 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025573-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pqyz87
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicraeanthus africanus Engl."
 ]
}

 The dataset includes 128 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025575-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rtuwp4
title: Occurrence Download

description: A dataset containing 11085 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arma custos (Fabricius, 1794)"
 ]
}

 The dataset includes 11085 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025574-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3x3sz
title: Occurrence Download

description: A dataset containing 1768 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potamididae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1768 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025576-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7zjry3
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicraeanthus taylorii J.J.de Wilde & Guillaumet"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025577-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ad333
title: Occurrence Download

description: A dataset containing 3120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nacellidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3120 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025578-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8wm22u
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicraeanthus zehnderi H.Hess"
 ]
}

 The dataset includes 26 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025579-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zfbfmr
title: Occurrence Download

description: A dataset containing 2434 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Spiranthes sinensis (Pers.) Ames"
 ]
}

 The dataset includes 2434 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025584-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qzqcce
title: Occurrence Download

description: A dataset containing 503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rissoidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 503 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025583-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/3565
title: zasca-sum
DOI: 10.25326/640
title: PARCS_CNRM_LUXEMBOURG_IOT_6min_L2

description: This dataset contains air temperature, air humidity, black globe temperature, wind and temperature/humidity measurements in  soil. These measurements have been done at jardin du Luxembourg in Paris during PARCS campaign with IoT sensors. All measurements are interpolated from 10min to 6min to be compared with 6 min data from RADOME stations (Météo-France network).
DOI: 10.15468/dl.y855bq
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anatomidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 90 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025585-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25326/641
title: PARCS_CNRM_MONTSOURIS_IOT_6min_L2

description: This dataset contains black globe temperature, wind and temperature/moisture measurements in  soil. These measurements have been done at Parc Montsouris in Paris during PARCS campaign with IoT sensors. All measurements are interpolated from 10min to 6min to be compared with 6 min data from RADOME stations (Météo-France network).
DOI: 10.15468/dl.enb7x5
title: Occurrence Download

description: A dataset containing 4125 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Occurrence dataset of birds in the Sihong Hongze Lake Wetland National Nature Reserve,Jiangsu, China"
 ]
}

 The dataset includes 4125 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025586-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25326/649
title: PARCS_CNRM_SQUARE-TEMPLE_6min_L2

description: This dataset contains air temperature, air humidity, air pressure, wind speed, black globe temperature, rainfall rate measured by conventional meteorological sensors and temperature/humidity in the soil measured by IoT sensors.  These measurements have been done at Square du Temple Elie Wiesel in Paris during PARCS campaign. Measurements are interpolated from 10min to 6min for IoT sensors in soil and 6min average for others meteorological data to be compared with 6 min data from RADOME stations (Météo-France network).
DOI: 10.48597/3qct-xp7r
title: Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/ftyp-rc9j
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/e2mg-92p8
title: Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/6hwq-sc28
title: Ammonia at High Muffles

description: Measurement of Ammonia at High Muffles
DOI: 10.48597/xea8-vd2u
title: Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/cwak-eh2q
title: Nitrate at High Muffles

description: Measurement of Nitrate at High Muffles
DOI: 10.48597/gjxj-4wgm
title: Nitric_acid at High Muffles

description: Measurement of Nitric_acid at High Muffles
DOI: 10.48597/shu8-ryy3
title: Ammonium at High Muffles

description: Measurement of Ammonium at High Muffles
DOI: 10.48597/esk3-28jd
title: Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/a3p6-4uws
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/pxsj-u6gb
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/3vqc-y2kq
title: Measurement of Ammonium at High Muffles

description: Measurement of Ammonium at High Muffles
DOI: 10.48597/4crt-xb3w
title: Measurement of Ammonia at High Muffles

description: Measurement of Ammonia at High Muffles
DOI: 10.48597/pb2f-fv4t
title: Measurement of Nitric_acid at High Muffles

description: Measurement of Nitric_acid at High Muffles
DOI: 10.48597/uefp-by5j
title: Measurement of Nitrate at High Muffles

description: Measurement of Nitrate at High Muffles
DOI: 10.48597/6euh-rydf
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.5281/zenodo.14194954
title: The raw data of Spatial muti-omics of glioma

description: Our files include the raw data from single-cell RNA sequencing, spatial transcriptomics sequencing, RNA  sequencing, and mass spectrometry analyses conducted in our study. Additionally, they contain clinical information for the patients involved in the single-cell RNA and spatial transcriptomics sequencing. These clinical data have been handled in compliance with privacy protection regulations to safeguard patient confidentiality. The raw data of the paper "Deciphering radial glial stem-like cells based on spatial multi-omics guides safe therapy in glioma".
DOI: 10.5281/zenodo.14194955
title: The raw data of Spatial muti-omics of glioma

description: Our files include the raw data from single-cell RNA sequencing, spatial transcriptomics sequencing, RNA  sequencing, and mass spectrometry analyses conducted in our study. Additionally, they contain clinical information for the patients involved in the single-cell RNA and spatial transcriptomics sequencing. These clinical data have been handled in compliance with privacy protection regulations to safeguard patient confidentiality. The raw data of the paper "Deciphering radial glial stem-like cells based on spatial multi-omics guides safe therapy in glioma".
DOI: 10.15468/dl.n9xcdw
title: Occurrence Download

description: A dataset containing 3395 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is birds-red-river-delta-seawater-reservoir"
 ]
}

 The dataset includes 3395 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025587-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/2a4m-vwuv
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/2m85-4axz
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/7chr-kmxy
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/7mqw-caht
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/7tf9-yhwv
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/8b2t-3pes
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/a8as-4w44
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.15468/dl.enuqjf
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Butumia marginalis G.Taylor"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025589-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/anvj-p2ae
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/gk2b-vjjw
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/hvrd-wr8z
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles
DOI: 10.48597/j7vh-mkr9
title: Measurement of Inorganics in air and particle phase at High Muffles

description: Measurement of Inorganics in air and particle phase at High Muffles