cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/pa2-apq-g32
title: Liparis liparis (Linnaeus, 1766)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/41r-bnb-8e4
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/55q-6ey-4ns
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1vg-n70-btm
title: Conulariida

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/e2x-1ms-qmg
title: Conularia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/app-872-tft
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/0bm-5ly-qf4
title: Conulariida

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/s2n-h5f-296
title: Conulariida

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/csp-lxj-c2s
title: Conularia cancellata Sandberger, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mqb-82p-t0e
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/493-4sb-4p1
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sk4-kcg-cwg
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g4v-3bp-hrg
title: Conularia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zg4-elc-m73
title: Conularia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9nq-zcv-chp
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fcf-kqe-msp
title: Conularia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5t9-d84-fkx
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ajv-e0v-mlg
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dd0-jyq-6hd
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/f5f-c6r-et4
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/7rx-xw3-g7v
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8lp-sgs-nye
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dm8-zwz-m20
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fw7-m92-jm6
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wt9-jfn-4n9
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/evc-e8r-b3v
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mwt-hx0-9vv
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6be-0kp-ctl
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/t1c-apl-rh9
title: Stelliporella parvistella (Roemer, 1861)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gts-m47-rcj
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pzj-1na-qqc
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/kav-ehk-kwc
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/m5w-x2f-x6q
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/l1f-pcx-mny
title: Wormsipora cf. hirsuta (Lindström, 1899)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pmt-67v-5pe
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/jq8-05z-6r2
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vxj-w0x-60f
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bsq-xs3-j65
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vj6-j6r-sdk
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vzx-tak-p0m
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xs0-55y-4al
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1wp-g34-yqa
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/e1e-62l-9r2
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4se-1l9-bmw
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/897-h7n-kpd
title: Wormsipora cf. hirsuta (Lindström, 1899)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/c0q-mg9-9a2
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/az8-rte-wxy
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bhk-qxn-9wm
title: Heliolitina

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/33n-r7r-rgg
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q3e-ezv-la6
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5ar-ybj-qdm
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/eh5-vbv-g51
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/444-wya-d4e
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/848-wdk-c1a
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/58g-xy6-l6k
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/n90-55b-ttm
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8lz-yld-674
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/95j-jtp-yhd
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5281/zenodo.14884614
title: Dataset and codes for paper: VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines

description: VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines.

VSOT is a method based on volume-surface optimization that is designed for the accurate structural analysis of dendritic reconstruction. VSOT accurately segments dendritic reconstructions into compartments, including spine, spine head and neck, by leveraging advanced optimization techniques that integrate local surface and global volumetric information. Our tests on public datasets of spine segmentation, as well as on a first-of-its-kind dataset of head-neck segmentation that we manually constructed, show that VSOT offers more accurate results than peer methods. When applied to a large EM dataset of different brain layers, VSOT reveals how the structure of dendrites varies across brain areas. Furthermore, we explored the structural relationships between neurons and astrocytes in tripartite synapses. With the newly developed computation methods, neuroscientists can exploit the large-scale volumetric EM data to address various scientific questions and advance the understanding of neural circuits.

Contents:

'performance_testing_level_1_segmentation.zip'

A ground truth dataset designed for testing the performance of dendritic spine and shaft segmentation. This data was acquired by converting the 3D reconstruction of dendrite #5 from the dataset published by Kasthuri et al. (2015)

'performance_testing_level_2_segmentation.zip'

Ground truth dataset for performance testing the spine head-neck segmentation. It contains over 700 dendritic spines that are segmented from the MICrONS dataset (Consortium et al. 2021) with annotations. It involves independent labeling of the cut between the spine head and spine neck by three annotators. Quality control was implemented by retaining only those that reached a consensus, resulting in 636 samples. Additionally, we included 67 stubby spines.

'segmentation_example_data.zip'

Demo data for the complete VSOT pipeline, featuring the segmentation of a single dendrite alongside the nearby astrocyte segmentation. Users can utilize this example data to evaluate the level-1 and level-2 segmentation and the quantification modules of VSOT. 

'results.zip'

Results for the two performance tests and the results after applying VSOT to the example dataset.

'VSOT-main.zip'

Codes for VSOT, containing the codes for preprocessing, level-1, level-2, experiments and quantification. It is also stored in Github https://github.com/yu-lab-vt/VSOT.git
DOI: 10.5281/zenodo.14884615
title: Dataset for paper: VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines

description: VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines.

VSOT is a method based on volume-surface optimization that is designed for the accurate structural analysis of dendritic reconstruction. VSOT accurately segments dendritic reconstructions into compartments, including spine, spine head and neck, by leveraging advanced optimization techniques that integrate local surface and global volumetric information. Our tests on public datasets of spine segmentation, as well as on a first-of-its-kind dataset of head-neck segmentation that we manually constructed, show that VSOT offers more accurate results than peer methods. When applied to a large EM dataset of different brain layers, VSOT reveals how the structure of dendrites varies across brain areas. Furthermore, we explored the structural relationships between neurons and astrocytes in tripartite synapses. With the newly developed computation methods, neuroscientists can exploit the large-scale volumetric EM data to address various scientific questions and advance the understanding of neural circuits.

Contents:

'performance_testing_level_1_segmentation.zip'

A ground truth dataset designed for testing the performance of dendritic spine and shaft segmentation. This data was acquired by converting the 3D reconstruction of dendrite #5 from the dataset published by Kasthuri et al. (2015)

'performance_testing_level_2_segmentation.zip'

Ground truth dataset for performance testing the spine head-neck segmentation. It contains over 700 dendritic spines that are segmented from the MICrONS dataset (Consortium et al. 2021) with annotations. It involves independent labeling of the cut between the spine head and spine neck by three annotators. Quality control was implemented by retaining only those that reached a consensus, resulting in 636 samples. Additionally, we included 67 stubby spines.

'segmentation_example_data.zip'

Demo data for the complete VSOT pipeline, featuring the segmentation of a single dendrite alongside the nearby astrocyte segmentation. Users can utilize this example data to evaluate the level-1 and level-2 segmentation and the quantification modules of VSOT. 

'results.zip'

Results for the two performance tests and the results after applying VSOT to the example dataset.
DOI: 10.5281/zenodo.15115542
title: Dataset and codes for paper: VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines

description: VSOT: Volume-Surface Optimization for Accurate Ultrastructure Analysis of Dendritic Spines.

VSOT is a method based on volume-surface optimization that is designed for the accurate structural analysis of dendritic reconstruction. VSOT accurately segments dendritic reconstructions into compartments, including spine, spine head and neck, by leveraging advanced optimization techniques that integrate local surface and global volumetric information. Our tests on public datasets of spine segmentation, as well as on a first-of-its-kind dataset of head-neck segmentation that we manually constructed, show that VSOT offers more accurate results than peer methods. When applied to a large EM dataset of different brain layers, VSOT reveals how the structure of dendrites varies across brain areas. Furthermore, we explored the structural relationships between neurons and astrocytes in tripartite synapses. With the newly developed computation methods, neuroscientists can exploit the large-scale volumetric EM data to address various scientific questions and advance the understanding of neural circuits.

Contents:

'performance_testing_level_1_segmentation.zip'

A ground truth dataset designed for testing the performance of dendritic spine and shaft segmentation. This data was acquired by converting the 3D reconstruction of dendrite #5 from the dataset published by Kasthuri et al. (2015)

'performance_testing_level_2_segmentation.zip'

Ground truth dataset for performance testing the spine head-neck segmentation. It contains over 700 dendritic spines that are segmented from the MICrONS dataset (Consortium et al. 2021) with annotations. It involves independent labeling of the cut between the spine head and spine neck by three annotators. Quality control was implemented by retaining only those that reached a consensus, resulting in 636 samples. Additionally, we included 67 stubby spines.

'segmentation_example_data.zip'

Demo data for the complete VSOT pipeline, featuring the segmentation of a single dendrite alongside the nearby astrocyte segmentation. Users can utilize this example data to evaluate the level-1 and level-2 segmentation and the quantification modules of VSOT. 

'results.zip'

Results for the two performance tests and the results after applying VSOT to the example dataset.

'VSOT-main.zip'

Codes for VSOT, containing the codes for preprocessing, level-1, level-2, experiments and quantification. It is also stored in Github https://github.com/yu-lab-vt/VSOT.git
DOI: 10.3535/47h-wfk-bdx
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ya8-v72-5t1
title: Homostius

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/f2e-njv-ehj
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/w01-6ky-he4
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gdw-p70-sc9
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vaq-1nn-wht
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/yem-c83-rtm
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pbm-gq6-zlv
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q8r-9sx-ylk
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5ev-wxx-h5b
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/meg-kfs-38k
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ema-xba-5wa
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/w79-gv6-lvy
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dab-lre-9td
title: Animalia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xyd-nrq-e18
title: Heliolitoidea

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2zf-7xq-v1k
title: Ampullaceana balthica (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/d2q-nxt-497
title: Pisidium amnicum (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9qp-pzr-g7r
title: igneous rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gsk-6j8-brm
title: Ancylus fluviatilis O. F. Müller, 1774

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/20c-dsk-bgp
title: Lymnaea stagnalis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/b0v-lqc-hzk
title: Ampullaceana dipkunensis (Gundrizer & Starobogatov, 1979)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8x0-cbt-f69
title: Bithynia leachii (Sheppard, 1823)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/prb-nw2-qw1
title: Saturnia (Eudia) pavonia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9qt-5c3-9bf
title: Saturnia (Eudia) pavonia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e5j-eh4-q6y
title: Drepana falcataria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2qv-fkv-a35
title: Watsonalla cultraria (Fabricius, 1775)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vzv-bca-sg9
title: Sphrageidus similis (Fuessly, 1775)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hmf-7a5-lgp
title: Lymantria (Porthetria) dispar (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m30-0wt-j86
title: Orgyia (Orgyia) antiqua (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/px6-xnt-cd8
title: Orgyia (Orgyia) antiqua (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8qb-hjy-nbj
title: Lymantria (Porthetria) dispar (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g4l-z80-kax
title: Euthrix (Euthrix) potatoria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x1s-b5s-rqp
title: Euthrix (Euthrix) potatoria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v5s-xjb-j1x
title: Sphrageidus similis (Fuessly, 1775)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1r0-rpk-c8g
title: Leucoma salicis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1t0-z4y-6ar
title: Saturnia (Eudia) pavonia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1xn-tqy-ghk
title: Aglia tau Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/50x-0bt-ddf
title: Orgyia (Orgyia) antiqua (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7rf-hb8-3h8
title: Lasiocampa quercus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kww-c4t-hrh
title: Euthrix (Euthrix) potatoria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/409-vyn-a5s
title: Malacosoma neustria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jkx-fv4-s3k
title: Wittia sororcula (Hufnagel, 1767)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mkf-4s2-zq3
title: Watsonalla binaria (Hufnagel, 1769)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/00c-wmk-y7z
title: Elachista chrysodesmella Zeller, 1850

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ncq-sh2-tq4
title: Habrosyne pyritoides (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/brz-vmj-2rc
title: Euthrix (Euthrix) potatoria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pwf-8f1-1c3
title: Habrosyne pyritoides (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/95x-sql-mff
title: Hipparchia semele Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jn6-t1n-tqc
title: Drepana falcataria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g6r-kh7-fhm
title: Collita griseola (Hübner, 1803)

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