cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.yzj6wu
title: Occurrence Download

description: A dataset containing 286 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lannea microcarpa Engl. & K.Krause"
 ]
}

 The dataset includes 286 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000007-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hqypen
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Indosasa shibataeaoides McClure"
 ]
}

 The dataset includes 84 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000008-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p462qh
title: Occurrence Download

description: A dataset containing 800 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lannea barteri (Oliv.) Engl."
 ]
}

 The dataset includes 800 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000006-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13361905
title: Towards Enhancing Field-Based Vegetation Monitoring: A Deep Learning Approach for Species Identification and Coverage Estimation from Ground-level Imagery

description: 🌿Species Identification and Coverage Estimation from Ground-level Imagery for Vegetation Monitoring 📷

This repository contains the data and code used in Müller, Puliti, and Breidenbach (2025) to train and apply deep learning models for species coverage estimation using ground-level imagery.

It includes:✅ A YOLOv8 object detection model for detecting frames in images and one species instance segmentation model for species identification and identifying and segmenting species.

✅ Method to parse instance segmentation masks to species-specific coverage estimates in images.

✅ The data used to train and evaluate the models

 

🚀 Workflow Overview

This demo provides a step-by-step approach for training and applying the models:

1️⃣ Training:



Train two models using labeled images:



Frame Object Detection (dataset: Frame_data)

Species Instance Segmentation (dataset: Species_segmentation_data)




2️⃣ Confidence Optimization:



Optimize the confidence threshold based on downstream cover estimation performance.


3️⃣ Inference:



Predict on test images (Species_cover_data_test).


4️⃣ Evaluation:



Compare predictions with field estimates (Field_data_NFI).


📌 The code has been tested on Windows with Python 3.10.

 

🛠 How to Run the Demo

Follow these steps to set up and run demo.ipynb:





 






# Create a new environmentconda create -n VegCover python=3.10

# Activate the environmentconda activate VegCover

# Install dependenciespip install -r requirements.txt

# Install Jupyter Labpip install jupyterlab

# Open the demo notebookjupyter-lab




 

📖 How to Cite

If you use this work, please cite:

Müller, P., Puliti, S., & Breidenbach, J. (2025). Towards Enhancing Field-Based Vegetation Monitoring: A Deep Learning Approach for Species Coverage Estimation from Ground-Level Imagery. Methods in Ecology and Evolution.

 

📜 License

This project is licensed under the GNU Affero General Public License v3.0 or later (AGPL-3.0-or-later).

🔹 Key points of this license:



You are free to use, modify, and distribute the software.

If you modify and deploy this software (even as a web service), you must share your modifications under the same AGPL-3.0-or-later license.

This ensures that improvements remain open-source and benefit the community.


📖 Full license text: GNU AGPL v3.0
DOI: 10.5281/zenodo.13361904
title: Towards Enhancing Field-Based Vegetation Monitoring: A Deep Learning Approach for Species Identification and Coverage Estimation from Ground-level Imagery

description: 🌿Species Identification and Coverage Estimation from Ground-level Imagery for Vegetation Monitoring 📷

This repository contains the data and code used in Müller, Puliti, and Breidenbach (2025) to train and apply deep learning models for species coverage estimation using ground-level imagery.

It includes:✅ A YOLOv8 object detection model for detecting frames in images and one species instance segmentation model for species identification and identifying and segmenting species.

✅ Method to parse instance segmentation masks to species-specific coverage estimates in images.

✅ The data used to train and evaluate the models

 

🚀 Workflow Overview

This demo provides a step-by-step approach for training and applying the models:

1️⃣ Training:



Train two models using labeled images:



Frame Object Detection (dataset: Frame_data)

Species Instance Segmentation (dataset: Species_segmentation_data)




2️⃣ Confidence Optimization:



Optimize the confidence threshold based on downstream cover estimation performance.


3️⃣ Inference:



Predict on test images (Species_cover_data_test).


4️⃣ Evaluation:



Compare predictions with field estimates (Field_data_NFI).


📌 The code has been tested on Windows with Python 3.10.

 

🛠 How to Run the Demo

Follow these steps to set up and run demo.ipynb:





 






# Create a new environmentconda create -n VegCover python=3.10

# Activate the environmentconda activate VegCover

# Install dependenciespip install -r requirements.txt

# Install Jupyter Labpip install jupyterlab

# Open the demo notebookjupyter-lab




 

📖 How to Cite

If you use this work, please cite:

Müller, P., Puliti, S., & Breidenbach, J. (2025). Towards Enhancing Field-Based Vegetation Monitoring: A Deep Learning Approach for Species Coverage Estimation from Ground-Level Imagery. Methods in Ecology and Evolution.

 

📜 License

This project is licensed under the GNU Affero General Public License v3.0 or later (AGPL-3.0-or-later).

🔹 Key points of this license:



You are free to use, modify, and distribute the software.

If you modify and deploy this software (even as a web service), you must share your modifications under the same AGPL-3.0-or-later license.

This ensures that improvements remain open-source and benefit the community.


📖 Full license text: GNU AGPL v3.0
DOI: 10.15468/dl.rf2k7q
title: Occurrence Download

description: A dataset containing 171674 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is United States of America",
 "DatasetKey is EOD – eBird Observation Dataset",
 "OccurrenceStatus is Present",
 "TaxonKey is Spinus tristis (Linnaeus, 1758)",
 "Year 1985-2000"
 ]
}

 The dataset includes 171674 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000145-250402095845217/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ab823p
title: Occurrence Download

description: A dataset containing 66589 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.datasetkey = '7b468209-8d5c-477b-b118-cdf04dde9912'
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 66589 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000002-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t4cuve
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Indosasa sinica C.D.Chu & C.S.Chao"
 ]
}

 The dataset includes 93 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000009-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.srkm48
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Indosasa crassiflora McClure"
 ]
}

 The dataset includes 24 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000010-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15125411
title: sulfate migration pattern after repairing the Ming Great Wall

description: Salinity deterioration is one of the most critical factors contributing to the degradation of pre- and post-rehabilitation earthen sites in Northwest China. This study utilized hemp-cut fiber-modified soil, a common material in restoration projects, to investigate the water and salt migration patterns of earthen sites after restoration and to clarify the mechanisms of salt deterioration in restored earthen sites. The migration rates and pathways of sodium sulfate in earthen sites before and after restoration are quantified by remodeling site soil specimens and restoration simulation specimens to clarify migration mechanisms from a microscopic perspective. The test results indicated that the rate of salt accumulation in the earthen sites significantly decreases, and the rate of salt damage slows after restoration with hemp-cut fiber-modified soil. Due to the rapid salt accumulation rate at the repair's edge, the hemp-cut fiber repair layer exhibits severe cracking. Although the rate of salt migration in each component changes after restoration, the migration pathways remain fundamentally the same. Under capillary action, the salt ascends to the maximum height along the edge. Then, the primary migration mode shifts to horizontal diffusion, accelerating the salt accumulation rate in the central area. Simultaneously, as salt accumulates at the top, the influence of gravity increases. More salt migrates downward, ultimately enriching the middle and upper layers of the site. This study can provide a reference for protecting against salt damage in earthen site restoration and for selecting and revising restoration materials.
DOI: 10.5281/zenodo.15125412
title: sulfate migration pattern after repairing the Ming Great Wall

description: Salinity deterioration is one of the most critical factors contributing to the degradation of pre- and post-rehabilitation earthen sites in Northwest China. This study utilized hemp-cut fiber-modified soil, a common material in restoration projects, to investigate the water and salt migration patterns of earthen sites after restoration and to clarify the mechanisms of salt deterioration in restored earthen sites. The migration rates and pathways of sodium sulfate in earthen sites before and after restoration are quantified by remodeling site soil specimens and restoration simulation specimens to clarify migration mechanisms from a microscopic perspective. The test results indicated that the rate of salt accumulation in the earthen sites significantly decreases, and the rate of salt damage slows after restoration with hemp-cut fiber-modified soil. Due to the rapid salt accumulation rate at the repair's edge, the hemp-cut fiber repair layer exhibits severe cracking. Although the rate of salt migration in each component changes after restoration, the migration pathways remain fundamentally the same. Under capillary action, the salt ascends to the maximum height along the edge. Then, the primary migration mode shifts to horizontal diffusion, accelerating the salt accumulation rate in the central area. Simultaneously, as salt accumulates at the top, the influence of gravity increases. More salt migrates downward, ultimately enriching the middle and upper layers of the site. This study can provide a reference for protecting against salt damage in earthen site restoration and for selecting and revising restoration materials.
DOI: 10.15468/dl.kbausp
title: Occurrence Download

description: A dataset containing 3490 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Macaca fuscata (Blyth, 1875)"
 ]
}

 The dataset includes 3490 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000012-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yfdghw
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.12758 15.76698,-96.11089 15.76698,-96.11089 15.78416,-96.12767 15.78449,-96.12758 15.77722,-96.12758 15.76698))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 309 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0199188-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kkmdnt
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Strychnos umbellata (Lour.) Merr.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046798-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gpzdux
title: Occurrence Download

description: A dataset containing 6562304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-180 66,180 66,180 90,-180 90,-180 66))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 6562304 records from 1079 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221796-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9gvuy3
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crepis auriculifolia Sieber ex Spreng.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079938-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m1djrm
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptodactylus viridis Jim & Spirandeli Cruz, 1973"
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046802-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc25k12w
title: CCDC 2012367: Experimental Crystal Structure Determination

description: Related Article: Shan Wang, Long Li, Yifei Zheng, Luqing Li, Yingcheng Wang, Fangzhi Peng, Zhihui Shao|2024|Org.Chem.Front.|11|3033|doi:10.1039/D4QO00358F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.tpqbqe
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Smilax chiapensis Lundell"
 ]
}

 The dataset includes 20 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0142869-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc25k13x
title: CCDC 2012368: Experimental Crystal Structure Determination

description: Related Article: Shan Wang, Long Li, Yifei Zheng, Luqing Li, Yingcheng Wang, Fangzhi Peng, Zhihui Shao|2024|Org.Chem.Front.|11|3033|doi:10.1039/D4QO00358F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.35ktbr
title: Occurrence Download

description: A dataset containing 331 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crataegus orientalis Pall. ex M.Bieb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 331 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079916-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xxoquj
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 {
 "or" : [
 "Country is Sweden",
 "Country is Slovakia",
 "Country is Poland"
 ]
 },
 "TaxonKey is Lynx lynx (Linnaeus, 1758)"
 ]
}

 The dataset includes 29 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046803-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc29wmmg
title: CCDC 2141716: Experimental Crystal Structure Determination

description: Related Article: Guohui Zeng, Hui Luo, Kai Jiang, Jianpeng Cai, Biaolin Yin|2024|Org.Chem.Front.|11|3165|doi:10.1039/D4QO00317A
description: Related Article: guohui zeng|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.huwz02
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Solanum pillahuatense Vargas"
 ]
}

 The dataset includes 26 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002011-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jggpuw
title: Occurrence Download

description: A dataset containing 109349 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Symphoricarpos albus (L.) K.Koch",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 109349 records from 620 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079913-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/gme-1jh-fsj
title: Graphium

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xn6-5pkq
title: PAN-00075452 - coin/coin-related, Edward I (1272-1307), penny

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00075452&lt;/p&gt;
description: Modified: 2021-02-22T15:27:28+01:00
DOI: 10.3535/bq4-6fs-j45
title: Hesperiidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r8t-s40-skn
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/swh-bhg-x0s
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kzs-182-836
title: Euthalia Hübner, 1819

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/laz-03d-djs
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rf5-2l8-qj9
title: Celaenorrhinus inaequalis Elwes & Edwards, 1897

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xn6-6waf
title: PAN-00069541 - cast hooked-clasp with one hook Group C

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00069541&lt;/p&gt;
description: Modified: 2020-06-18T11:26:08+02:00
DOI: 10.3535/e4n-ph4-s8m
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q7a-1hr-19w
title: Riodinidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.