cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13897937
title: Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues - Data processing manual

description: Here we provide test datasets and a training manual for the parameter optimization with eSRRF. 

The training manual will guide users through an eSRRF paramenter optimization routine and quantiative image quality assesment with both, the ImagJ-Plugin NanoJ-eSRRF (Chapter 1) and the python implementation NanoPyx-eSRRF (Chapter 2). By showcasing the optimization routine on three differnt test dataset (Chapter 3), providing intermediate results and expected outcome, the users can eaisily learn how to find the optimal processing parameters for eSRRF processing.

Three samples are provided to showcase the eSRRF reconstruction process:

1. Microtubules sample: Set01_DNA-PAINT_Microtubules.tif

DNA-PAINT microscopy measurement of immunolabeled microtubules in fixed COS-7 cells, showing 0.121 localizations per frame and µm^2 (data published in Laine and Heil et al.)

108x90 pixels, 500 frames, pixel size: 160 nm 

2. Kidney sample: Set02_KidneySDNephrinExM.tif

ExM of human kidney biopsies stained with nephrin (data published in Kylies et al.)

150x150 pixels, 200 frames, pixel size: 102 nm 

3. Single emitters simulation: Set03_simulation_groundTruth_2p5Sigma - Fluorescence stack_Avg5.tif

Simulated individual molecules emitting placed on concentric rings with radii increasing by 220 nm steps. On each ring the molecules are separated by 57.5, 115, 173, 230, 288 and 345 nm, respectively (data published in Laine and Heil et al.)

33x33 pixels, 100 frames, pixel size: 100 nm 

4. Test dataset for drift/vibration correction: Set04_ExSRRF_eSRRF_vibration_correction_practice_dataset.tif

EsM of human kidney biopsies stained with nephrin (data published in Kylies et al.)

100x100 pixels, 200 frames, pixel size: 102 nm

5. Test dataset for photobleaching: Set05_Photobleaching.tif

ExM of 120 nm Nanorulers (data published in Kylies et al.)

150x150 pixels, 75 frames, pixel size: 64 nm

 

Jupyter-Notebook: ridge_detection.ipynb

With this notebook qantitative image analyis of sturctures resolved with ExSRRF can be performed.

Such as:



calculation of the target structure density. 

identifying areas with high inter-ridge spacing by maping the distance to the nearest ridge based on Euclidean distance transform. 

measuring the spatial uniformity of the structure of interest by examining the distribution of the local densities and the distances to the nearest ridge.
DOI: 10.5281/zenodo.13837705
title: Data linked to the publication "NbS for CO2 emissions offsetting; a case study from Chania city center, Crete".

description: This record contains background data linked to the publication "NbS for CO2 emissions offsetting; a case study from Chania city center, Crete".

The datasets included are ENVI-met output files, spreadsheets with CO2 sequestration and Temperature data, derived from the ENVI-met output files as well as simulation results of the i-tree planting tool.

Please read the README files for explanation of the datasets included in this record.
DOI: 10.15468/dl.pm6bd9
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Deinbollia mezilii D.W.Thomas & D.J.Harris"
 ]
}

 The dataset includes 40 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000004-241007104925546/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.27179113
title: Phymateus_saxosus_01_movie_tiff_bin4.mp4 from Inter-and intra-specific variation in grasshopper (Orthoptera: Acrididea) molar form: implications for dietary ecology

description: Video of a microCT scanned grasshopper head (Phymateus saxosus 01)
DOI: 10.34740/kaggle/dsv/9566764
title: Full TMDB Movies Dataset 2024 (1M Movies)
DOI: 10.6084/m9.figshare.27179122
title: ESM_figures.pdf from Inter-and intra-specific variation in grasshopper (Orthoptera: Acrididea) molar form: implications for dietary ecology

description: Figures of microCT scanning setup and worn/unworn molar
DOI: 10.6084/m9.figshare.27179122.v1
title: ESM_figures.pdf from Inter-and intra-specific variation in grasshopper (Orthoptera: Acrididea) molar form: implications for dietary ecology

description: Figures of microCT scanning setup and worn/unworn molar
DOI: 10.15468/dl.u8a37s
title: Occurrence Download

description: A dataset containing 54168 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paeoniaceae"
 ]
}

 The dataset includes 54168 records from 728 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000003-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qbcudo
title: Occurrence Download

description: A dataset containing 40104 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Malus domestica (Suckow) Borkh."
 ]
}

 The dataset includes 40104 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-150831095807960/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9m2r4v
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus sciadophorus Franch."
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036566-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wsdw8n
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((85.88113 17.15245,110.11887 17.15245,110.11887 26.84755,85.88113 26.84755,85.88113 17.15245))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Najas tenuis Magnus"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0334077-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hj6xjj
title: Occurrence Download

description: A dataset containing 2293 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tulipa gesneriana L."
 ]
}

 The dataset includes 2293 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzfb9c
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Senecio tacuaremboensis Arechav."
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192223-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqnr47
title: Occurrence Download

description: A dataset containing 6976 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((119.87576 1.21427,118.77905 -1.05892,118.12102 -3.71098,119.35732 -5.86453,123.84388 -5.44579,123.64448 -2.47468,125.37928 2.29104,119.87576 1.21427))",
 "TaxonKey is Polypodiopsida"
 ]
}

 The dataset includes 6976 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050564-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qqnr2s
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Piper tenuinerve C.DC."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192224-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kwqxai
title: Occurrence Download

description: A dataset containing 1253 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Exaerete smaragdina (Guérin-Méneville, 1844)"
 ]
}

 The dataset includes 1253 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cu2xzv
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilea striata Urb."
 ]
}

 The dataset includes 35 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192225-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.63jyca
title: Occurrence Download

description: A dataset containing 44367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen, Occurrence evidence, Machine Observation)",
 "Continent is North America",
 "OccurrenceStatus is Present",
 "TaxonKey is Didelphimorphia"
 ]
}

 The dataset includes 44367 records from 191 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005260-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c85mtz
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-135.71068 -31.28427,5.71068 -31.28427,5.71068 25.28427,-135.71068 25.28427,-135.71068 -31.28427))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Najas arguta Kunth"
 ]
}

 The dataset includes 88 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0334033-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehcacn
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dypsis intermedia Beentje"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ukwh0t
title: Occurrence Download

description: A dataset containing 1333 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tamandua mexicana (Saussure, 1860)"
 ]
}

 The dataset includes 1333 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013119-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f9pgps
title: Occurrence Download

description: A dataset containing 278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The New York Botanical Garden Herbarium (NY)",
 "RecordedBy is G. W. Carver"
 ]
}

 The dataset includes 278 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005262-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h8povn
title: Occurrence Download

description: A dataset containing 5936 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus strobus L."
 ]
}

 The dataset includes 5936 records from 176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5gvqgh
title: Occurrence Download

description: A dataset containing 1644 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Fasciola hepatica Linnaeus, 1758"
 ]
}

 The dataset includes 1644 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013938-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3hzz0g
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lagothrix poeppigii Schinz, 1844"
 ]
}

 The dataset includes 93 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036624-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ny9flw
title: Occurrence Download

description: A dataset containing 68179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ceratophyllum L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 68179 records from 346 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d6rczs
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rubus selleanus Helwig"
 ]
}

 The dataset includes 21 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192226-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.krx44c
title: Occurrence Download

description: A dataset containing 1342 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mitu tomentosum (Spix, 1825)"
 ]
}

 The dataset includes 1342 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046585-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rub39m
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is South Africa",
 "Geometry POLYGON((-7.03501 -37.52082,53.03501 -37.52082,53.03501 -13.47918,-7.03501 -13.47918,-7.03501 -37.52082))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Indigofera cryptantha var. cryptantha"
 ]
}

 The dataset includes 74 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036561-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a4qc5x
title: Occurrence Download

description: A dataset containing 2960 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Artemisia tridentata Nutt.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2960 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-171020152545675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgqjsj
title: Occurrence Download

description: A dataset containing 871 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Haemaphysalis flava Neumann, 1897"
 ]
}

 The dataset includes 871 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054299-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fex3a5
title: Occurrence Download

description: A dataset containing 731 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lagurus lagurus (Pallas, 1773)"
 ]
}

 The dataset includes 731 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048178-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x9xszi
title: Occurrence Download

description: A dataset containing 274 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Uredo rangelii J.A.Simpson, K.Thomas & Grgur.",
 "TaxonKey is Puccinia psidii G.Winter"
 ]
}

 The dataset includes 274 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-171025204727650/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gyxgbv
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Grammonota maritima Emerton, 1925"
 ]
}

 The dataset includes 88 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059298-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mwa92e
title: Occurrence Download

description: A dataset containing 9512 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Araneae"
 ]
}

 The dataset includes 9512 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006651-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nx2ug7
title: Occurrence Download

description: A dataset containing 90576586 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Canada",
 "Country is New Zealand",
 "Country is Australia",
 "Country is United Kingdom of Great Britain and Northern Ireland"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Chordata",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 90576586 records from 993 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002542-171113114016250/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ku7gar
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphrasia portae Freyn, 1893",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297102-210914110416597/datasets/export for details.
DOI: 10.15468/dl.zpuaxt
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Syngonanthus pulvinellus Moldenke"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003735-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4yz5mt
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Pseudancistrus kwinti Willink, Mol & Chernoff, 2010)"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013898-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pzbt6m
title: Occurrence Download

description: A dataset containing 551 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptodactylus longirostris Boulenger, 1882"
 ]
}

 The dataset includes 551 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0297112-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9xh9pd
title: Occurrence Download

description: A dataset containing 290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer laurinum Hassk.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 290 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013897-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhapp2
title: Occurrence Download

description: A dataset containing 584 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Syngonanthus tenuis (Kunth) Ruhland"
 ]
}

 The dataset includes 584 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003772-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dqku5w
title: Occurrence Download

description: A dataset containing 22348 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diptera",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is 2010",
 "Country is United Kingdom of Great Britain and Northern Ireland"
 ]
}

 The dataset includes 22348 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0309575-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.um9sc4
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Syngonanthus schwackei Ruhland"
 ]
}

 The dataset includes 17 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003752-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.