Datasets:

ArrojoeDrigoLab
/

quantem-base-model-sources

Dataset stringlengths 13 214	Experiment stringlengths 14 76	Dataset DOI / URL stringlengths 32 128	Grouping stringclasses 3 values	2D images int64 0 5.2k	3D acquisitions int64 0 358	Training tiles int64 0 17.6k
Desmosomes in A431 Cells FIB-SEM Volume	A431 Cell Desmosome FIB-SEM	https://openorganelle.janelia.org/datasets/aic_desmosome-1	Public	0	1	108
Desmosomes in A431 Cells - aic_desmosome-2 (FIB-SEM)	A431 Cell Desmosome-ER FIB-SEM	https://doi.org/10.25378/janelia.22670176	Public	0	1	582
Desmosomes in A431 Cells - aic_desmosome-3 (FIB-SEM)	A431 Cell Desmosome-ER FIB-SEM	https://doi.org/10.25378/janelia.22675078	Public	0	1	716
Data set 01 - Giardia lamblia adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11196419	Public	0	1	308
Data set 02 - Giardia lamblia adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11197168	Public	0	1	320
Data set 04 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11198586	Public	0	1	400
Data set 05 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11198691	Public	0	1	400
Data set 06 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11199320	Public	0	1	400
Data set 07 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11199433	Public	0	1	352
Data set 08 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11202406	Public	0	1	360
Data set 09 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11203027	Public	0	2	640
Data set 10 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11203782	Public	0	1	391
An Aedes aegypti mosquito antennal lobe EM dataset	Aedes aegypti Antennal Lobe ssTEM	https://doi.org/10.60533/boss-2025-gcyr	Public	0	1	400
Cali 2018 aging mouse cortex FIB-SEM volumes	Aging Mouse Cortex FIB-SEM	https://doi.org/10.5061/dryad.bh78sn5	Public	0	6	51
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 1	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12585	Public	0	1	210
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 2	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12586	Public	0	1	400
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 3	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12587	Public	0	1	400
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 4b	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12591	Public	0	1	288
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 5 part 1	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12592	Public	0	1	100
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 5 part 2	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12610	Public	0	1	78
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 6	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12609	Public	0	1	40
Supporting data for "Socially regulated developmental plasticity in the color pattern of an anemonefish"	Anemonefish Skin TEM	https://doi.org/10.5281/zenodo.16400562	Public	31	0	324
SBF-SEM micrographs of A. algerae microsporidia spores, 45 min germination	Anncaliia algerae Spore Germination SBF-SEM	https://doi.org/10.6019/EMPIAR-11368	Public	0	1	400
SBF-SEM micrographs of A. algerae microsporidia spores, 5 min germination	Anncaliia algerae Spore Germination SBF-SEM	https://doi.org/10.6019/EMPIAR-11367	Public	0	3	1,200
SBF-SEM micrographs of A. algerae spores, Ungerminated	Anncaliia algerae Ungerminated Spores SBF-SEM	https://doi.org/10.6019/EMPIAR-11369	Public	0	1	400
Dataset of microscopy (Confocal and electron) - Outer epidermal edges mediate cell-cell adhesion for tissue integrity in plants	Arabidopsis Hypocotyl Epidermis Cell Adhesion TEM	https://doi.org/10.5281/zenodo.15125559	Public	476	0	1,895
Arabidopsis Root Phloem SBF-SEM Volumes	Arabidopsis Root Phloem SBF-SEM	https://doi.org/10.6019/EMPIAR-10442	Public	0	4	464
Ultrastructure description of the spermatozoa of the Amazon bonytongue Arapaima gigas (Schinz, 1822)	Arapaima gigas Spermatozoa	https://doi.org/10.5281/zenodo.8359643	Public	20	0	19
BANC Adult Drosophila CNS EM Volume	BANC Adult Drosophila CNS Connectome ssTEM	https://doi.org/10.60533/boss-2025-941r	Public	0	1	220
Volume electron microscopy reveals bacterial endosymbiosis within host mitochondria	Bacterial Endosymbiosis in Host Mitochondria vEM	https://www.ebi.ac.uk/biostudies/studies/S-BIAD2413	Public	0	13	690
Borrelia burgdorferi between neighbouring endothelial cells in a lymphatic capillary	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30043093.v1	Public	0	1	51
Borrelia burgdorferi engulfed by a neutrophil	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042721.v1	Public	0	1	100
Borrelia burgdorferi in contact with the pericyte projection and the fibroblast	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042805.v1	Public	0	1	137
Borrelia burgdorferi partially enclosed within a lymphatic capillary of an endothelial cell	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042739.v1	Public	0	1	19
Borrelia burgdorferi under a pericyte in dorsal skin	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30041983.v2	Public	0	1	54
Borrelia burgdorferi within a collagen bundle in mouse ear	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042088.v1	Public	0	1	18
Immune cells migrating from the vein in dorsal skin	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042151.v1	Public	0	1	400
Multisite adhesion of Borrelia burgdorferi to the blood capillary surface in dorsal skin	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042646.v1	Public	0	1	80
Pericyte targeting by Borrelia burgdorferi	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042550.v1	Public	0	1	64
Transcellular migration of Borrelia burgdorferi through a lymphatic capillary endothelial cell	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30043204.v1	Public	0	1	19
C. elegans Anterior Pharynx ssTEM	C. elegans Anterior Pharynx ssTEM	https://doi.org/10.60533/BOSS-2015-FBTX	Public	0	1	400
Witvliet 2020 Dataset 1 L1 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 2 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 3 L1 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 4 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 5 L2 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 6 L3 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 7 Young Adult C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 8 Young Adult C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Entire C. elegans dauer larva (e1370) volume	C. elegans Dauer Larva FIB-SEM	https://doi.org/10.25378/janelia.20376591	Public	0	1	219
Yim Choe Bae 2024 C. elegans Dauer Nerve Ring TEM	C. elegans Dauer Nerve Ring TEM	https://doi.org/10.60533/BOSS-2023-RTPH	Public	0	1	400
White et al. 1986 C. elegans N2U Nerve Ring	C. elegans Nervous System Connectome TEM	https://doi.org/10.60533/boss-1986-745j	Public	0	1	239
Overexpression of an ALS-associated FUS mutation in C. elegans disrupts NMJ morphology and leads to defective neuromuscular transmission	C. elegans Neuromuscular Junction ALS-FUS ET	https://doi.org/10.5061/dryad.9ghx3ffg0	Public	0	6	37
COS-7 cell overexpressing ER and mitochondria markers for CLEM	COS-7 Cell ER & Mitochondria FIB-SEM	https://doi.org/10.25378/janelia.13123385	Public	0	1	71
FIB-SEM Dataset (Obara + Nixon-Abell et al., 2023)	COS-7 Cell ER-Mitochondria Contact Site FIB-SEM	https://doi.org/10.25378/janelia.24502954.v1	Public	0	1	332
COS-7 Cell FIB-SEM Volume	COS-7 Cell FIB-SEM	https://doi.org/10.25378/janelia.24943716	Public	0	1	358
Interphase COS-7 Cell FIB-SEM Volume	COS-7 Cell FIB-SEM (Xu 2021)	https://doi.org/10.25378/janelia.24944559	Public	0	1	208
C. elegans motor circuit serial-section EM volumes	Caenorhabditis elegans Motor Circuit SEM	https://doi.org/10.60533/BOSS-2022-1JI1	Public	0	5	1,592
Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network	Cal51 Cell Organelle Biogenesis Knockout FIB-SEM	https://doi.org/10.6019/EMPIAR-11695	Public	0	6	435
SBF-SEM datasets related to the manuscript "Trans-cellular tunnels induced by the fungal pathogen Candida albicans facilitate invasion through successive epithelial cells without host damage" by Lachat et al, 2022.	Candida albicans Epithelial Invasion SBF-SEM	https://doi.org/10.5281/zenodo.5776104	Public	0	11	450
Enigmatic tubular ultrastructure in the bacterial defensive symbiont of the Asian citrus psyllid Diaphorina citri	Candidatus Profftella armatura Tubular Ultrastructure SBF-SEM	https://doi.org/10.6084/m9.figshare.29371466.v2	Public	0	2	80
Transmission Electron Microscopy Tilt Series Data of Chondrocyte Primary Cilia in situ	Chicken Chondrocyte Primary Cilia ET	https://doi.org/10.5281/zenodo.4592614	Public	0	1	1
Chicken Embryonic Heart Multiscale Imaging	Chicken Embryonic Heart SBF-SEM	https://doi.org/10.5061/dryad.hdr7sqvg5	Public	0	4	450
Dataset- Creating a Virtual Leaf	Chickpea Leaf SBF-SEM	https://doi.org/10.5281/zenodo.7943403	Public	0	2	160
Chlamydomonas Cryo-Slice and View on Thermo Scientific Helios 5 Hydra PFIB	Chlamydomonas Cryo FIB-SEM	https://doi.org/10.6019/EMPIAR-11275	Public	0	1	18
Cryo-FIB-SEM data on Chlamydomonas reinhardtii cells	Chlamydomonas reinhardtii Cryo-FIB-SEM	https://doi.org/10.6019/EMPIAR-10870	Public	0	2	12
Subcellular architecture collodaria photosymbiosis	Collodaria Photosymbiosis FIB-SEM	https://doi.org/10.6019/EMPIAR-10738	Public	0	7	506
FIB-SEM Chinese Hamster Ovary cell line sample dataset	Contextual High-throughput vEM Acquisition FIB-SEM	https://doi.org/10.6019/EMPIAR-12660	Public	0	1	96
FIB-SEM Mouse kidney tissue samples	Contextual High-throughput vEM Acquisition FIB-SEM	https://doi.org/10.6019/EMPIAR-12674	Public	0	1	24
FIB-SEM Nicotiana benthamiana epidermal cell	Contextual High-throughput vEM Acquisition FIB-SEM	https://doi.org/10.6019/EMPIAR-12659	Public	0	1	4
FIB-SEM Nicotiana benthamiana epidermal cell - conventional acquisition	Contextual High-throughput vEM Acquisition FIB-SEM	https://doi.org/10.6019/EMPIAR-12662	Public	0	1	36
FIB-SEM Rat brain tissue samples	Contextual High-throughput vEM Acquisition FIB-SEM	https://doi.org/10.6019/EMPIAR-12675	Public	0	1	88
FIB-SEM Trypanosoma cruzi cell samples	Contextual High-throughput vEM Acquisition FIB-SEM	https://doi.org/10.6019/EMPIAR-12661	Public	0	1	24
3D imaging and quantitative analysis of digestive glands morphogenesis during crustacean development: application of micro-CT, light and electron microscopy	Crustacean Digestive Gland Morphogenesis TEM	https://doi.org/10.5281/zenodo.19369446	Public	7	0	7
Cultured mouse cerebellar granule neurons (jrc_mus-granule-neurons-2)	Cultured Mouse Cerebellar Granule Neuron FIB-SEM (jrc_mus-granule-neurons-2)	https://doi.org/10.25378/janelia.24222868	Public	0	1	79
Cultured mouse cerebellar granule neurons (jrc_mus-granule-neurons-3)	Cultured Mouse Cerebellar Granule Neuron FIB-SEM (jrc_mus-granule-neurons-3)	https://doi.org/10.25378/janelia.24222892	Public	0	1	397
DeepFocus Dataset 1.0	DeepFocus SEM Focus and Astigmatism Benchmark	https://doi.org/10.5281/zenodo.8416524	Public	47	0	47
P14 (d1) L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/P14_L4_AG_15-09-2015-5fce19f10100007c00cfaff0/view	Public	0	1	297
P14 (d2) L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/P14_L4_n2_AG_08-12-2016-5fce19f10100007c00cfafef/view	Public	0	1	311
P14 L2/3 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/P14_L23_AG_v3_17-03-2016-5fce1a690100007c00cfaff2/view	Public	0	1	240
P5 L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/2020-06-12-p5-align2-600590b70100001900bd2d33/view	Public	0	1	400
P7 (d1) L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/P7_L4_AG_27-05-2017_v1-5fce18c50100001900cfafec/view	Public	0	1	400
P7 (d2, control) L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/2020-05-19-st045-align-600590860100008900bd2d31/view	Public	0	1	400
P9 (d1) L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/AG_P9_L4_30-06-2016-5fce193d0100006000cfafed/view	Public	0	1	400
P9 (d2) L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/P9_L4_OldVerios_24-12-2015_v1-5fce19b50100007a00cfafee/view	Public	0	1	328
P9 (d3, control) L4 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/2020-06-06-st048-align-600590850100008000bd2d30/view	Public	0	1	400
P9 L2/3 Barrel Cortex	Developing Mouse Barrel Cortex Interneuron Synaptogenesis SBF-SEM	https://webknossos.org/datasets/2016-07-07_P9_L23_v1-5fce1a2d0100007a00cfaff1/view	Public	0	1	358
Developing retina in zebrafish 55 hpf larval eye	Developing Zebrafish Retina SBF-SEM	https://doi.org/10.6019/EMPIAR-11759	Public	0	1	36
Diplonemid Protist TEM Images	Diplonemid Protist TEM	https://doi.org/10.5281/zenodo.16882378	Public	46	0	210
Dividing HeLa Cell FIB-SEM at 11.2 min after anaphase onset	Dividing HeLa Cell FIB-SEM	https://doi.org/10.6019/EMPIAR-10109	Public	0	1	58
Dividing HeLa Cell FIB-SEM at 3.1 min after anaphase onset	Dividing HeLa Cell FIB-SEM	https://doi.org/10.6019/EMPIAR-10100	Public	0	1	186
Dividing HeLa Cell FIB-SEM at 3.9 min after anaphase onset	Dividing HeLa Cell FIB-SEM	https://doi.org/10.6019/EMPIAR-10102	Public	0	1	130
Dividing HeLa Cell FIB-SEM at 4.3 min after anaphase onset	Dividing HeLa Cell FIB-SEM	https://doi.org/10.6019/EMPIAR-10103	Public	0	1	68
Dividing HeLa Cell FIB-SEM at 6.3 min after anaphase onset	Dividing HeLa Cell FIB-SEM	https://doi.org/10.6019/EMPIAR-10101	Public	0	1	315
FIB-SEM of a dividing cell at 5.3 min after anaphase onset	Dividing HeLa Cell FIB-SEM	https://doi.org/10.6019/EMPIAR-10104	Public	0	1	63
FIB-SEM of a dividing cell at 5.7 min after anaphase onset	Dividing HeLa Cell FIB-SEM	https://doi.org/10.6019/EMPIAR-10105	Public	0	1	173
Drosophila brain: Fan-shaped body	Drosophila Brain Fan-Shaped Body FIB-SEM	https://doi.org/10.25378/janelia.24222598	Public	0	1	12
Drosophila brain: protocerebral bridge	Drosophila Brain Protocerebral Bridge FIB-SEM	https://doi.org/10.25378/janelia.24222652	Public	0	1	17
Drosophila Hemibrain FIB-SEM Volume	Drosophila Central Brain Hemibrain FIB-SEM	https://webknossos.org/datasets/flyem_hemibrain-6128c212010000a100ca0fd6/view	Public	0	1	333
Drosophila ellipsoid body	Drosophila Ellipsoid Body FIB-SEM	https://doi.org/10.25378/janelia.24221404	Public	0	1	12

End of preview. Expand in Data Studio

QuantEM — base model data sources

Every dataset in the corpus the QuantEM ViT-B encoder was pretrained on: public repository holdings, data contributed by external laboratories through the QuantEM outreach campaign, and in-house acquisitions.

Emitted verbatim from Supplementary Table 2 of the QuantEM manuscript — 657 rows. Please cite the original sources listed here alongside QuantEM; rows carry a DOI or repository URL where one exists.

ArrojoeDrigoLab/quantem — the released model weights
ArrojoeDrigoLab/quantem-organelle-model-sources — the other sources table

Breakdown by grouping

Row counts over the table below.

Grouping	Datasets
Public	502
Outreach	117
Internal	38

Sources

First 60 of 657 rows — browse or download the full table in the Data Studio viewer above, or from sources.csv.

Dataset	Experiment	Dataset DOI / URL	Grouping	2D images	3D acquisitions	Training tiles
Desmosomes in A431 Cells FIB-SEM Volume	A431 Cell Desmosome FIB-SEM	https://openorganelle.janelia.org/datasets/aic_desmosome-1	Public	0	1	108
Desmosomes in A431 Cells - aic_desmosome-2 (FIB-SEM)	A431 Cell Desmosome-ER FIB-SEM	https://doi.org/10.25378/janelia.22670176	Public	0	1	582
Desmosomes in A431 Cells - aic_desmosome-3 (FIB-SEM)	A431 Cell Desmosome-ER FIB-SEM	https://doi.org/10.25378/janelia.22675078	Public	0	1	716
Data set 01 - Giardia lamblia adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11196419	Public	0	1	308
Data set 02 - Giardia lamblia adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11197168	Public	0	1	320
Data set 04 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11198586	Public	0	1	400
Data set 05 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11198691	Public	0	1	400
Data set 06 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11199320	Public	0	1	400
Data set 07 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11199433	Public	0	1	352
Data set 08 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11202406	Public	0	1	360
Data set 09 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11203027	Public	0	2	640
Data set 10 - HeLa adherent SBF-SEM series	Adherent Cell SBF-SEM	https://doi.org/10.5281/zenodo.11203782	Public	0	1	391
An Aedes aegypti mosquito antennal lobe EM dataset	Aedes aegypti Antennal Lobe ssTEM	https://doi.org/10.60533/boss-2025-gcyr	Public	0	1	400
Cali 2018 aging mouse cortex FIB-SEM volumes	Aging Mouse Cortex FIB-SEM	https://doi.org/10.5061/dryad.bh78sn5	Public	0	6	51
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 1	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12585	Public	0	1	210
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 2	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12586	Public	0	1	400
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 3	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12587	Public	0	1	400
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 4b	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12591	Public	0	1	288
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 5 part 1	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12592	Public	0	1	100
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 5 part 2	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12610	Public	0	1	78
Horizontal cell connectivity in the anchovy retina - a 3D electron microscopic study - Scan 6	Anchovy Retina Horizontal Cell Connectivity	https://doi.org/10.6019/EMPIAR-12609	Public	0	1	40
Supporting data for "Socially regulated developmental plasticity in the color pattern of an anemonefish"	Anemonefish Skin TEM	https://doi.org/10.5281/zenodo.16400562	Public	31	0	324
SBF-SEM micrographs of A. algerae microsporidia spores, 45 min germination	Anncaliia algerae Spore Germination SBF-SEM	https://doi.org/10.6019/EMPIAR-11368	Public	0	1	400
SBF-SEM micrographs of A. algerae microsporidia spores, 5 min germination	Anncaliia algerae Spore Germination SBF-SEM	https://doi.org/10.6019/EMPIAR-11367	Public	0	3	1200
SBF-SEM micrographs of A. algerae spores, Ungerminated	Anncaliia algerae Ungerminated Spores SBF-SEM	https://doi.org/10.6019/EMPIAR-11369	Public	0	1	400
Dataset of microscopy (Confocal and electron) - Outer epidermal edges mediate cell-cell adhesion for tissue integrity in plants	Arabidopsis Hypocotyl Epidermis Cell Adhesion TEM	https://doi.org/10.5281/zenodo.15125559	Public	476	0	1895
Arabidopsis Root Phloem SBF-SEM Volumes	Arabidopsis Root Phloem SBF-SEM	https://doi.org/10.6019/EMPIAR-10442	Public	0	4	464
Ultrastructure description of the spermatozoa of the Amazon bonytongue Arapaima gigas (Schinz, 1822)	Arapaima gigas Spermatozoa	https://doi.org/10.5281/zenodo.8359643	Public	20	0	19
BANC Adult Drosophila CNS EM Volume	BANC Adult Drosophila CNS Connectome ssTEM	https://doi.org/10.60533/boss-2025-941r	Public	0	1	220
Volume electron microscopy reveals bacterial endosymbiosis within host mitochondria	Bacterial Endosymbiosis in Host Mitochondria vEM	https://www.ebi.ac.uk/biostudies/studies/S-BIAD2413	Public	0	13	690
Borrelia burgdorferi between neighbouring endothelial cells in a lymphatic capillary	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30043093.v1	Public	0	1	51
Borrelia burgdorferi engulfed by a neutrophil	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042721.v1	Public	0	1	100
Borrelia burgdorferi in contact with the pericyte projection and the fibroblast	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042805.v1	Public	0	1	137
Borrelia burgdorferi partially enclosed within a lymphatic capillary of an endothelial cell	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042739.v1	Public	0	1	19
Borrelia burgdorferi under a pericyte in dorsal skin	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30041983.v2	Public	0	1	54
Borrelia burgdorferi within a collagen bundle in mouse ear	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042088.v1	Public	0	1	18
Immune cells migrating from the vein in dorsal skin	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042151.v1	Public	0	1	400
Multisite adhesion of Borrelia burgdorferi to the blood capillary surface in dorsal skin	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042646.v1	Public	0	1	80
Pericyte targeting by Borrelia burgdorferi	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30042550.v1	Public	0	1	64
Transcellular migration of Borrelia burgdorferi through a lymphatic capillary endothelial cell	Borrelia burgdorferi in Mouse Skin Vasculature SBF-SEM	https://doi.org/10.6084/m9.figshare.30043204.v1	Public	0	1	19
C. elegans Anterior Pharynx ssTEM	C. elegans Anterior Pharynx ssTEM	https://doi.org/10.60533/BOSS-2015-FBTX	Public	0	1	400
Witvliet 2020 Dataset 1 L1 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 2 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 3 L1 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 4 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 5 L2 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 6 L3 C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 7 Young Adult C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Witvliet 2020 Dataset 8 Young Adult C. elegans Brain	C. elegans Brain Postnatal Development	https://doi.org/10.60533/BOSS-2020-FQI7	Public	0	1	400
Entire C. elegans dauer larva (e1370) volume	C. elegans Dauer Larva FIB-SEM	https://doi.org/10.25378/janelia.20376591	Public	0	1	219
Yim Choe Bae 2024 C. elegans Dauer Nerve Ring TEM	C. elegans Dauer Nerve Ring TEM	https://doi.org/10.60533/BOSS-2023-RTPH	Public	0	1	400
White et al. 1986 C. elegans N2U Nerve Ring	C. elegans Nervous System Connectome TEM	https://doi.org/10.60533/boss-1986-745j	Public	0	1	239
Overexpression of an ALS-associated FUS mutation in C. elegans disrupts NMJ morphology and leads to defective neuromuscular transmission	C. elegans Neuromuscular Junction ALS-FUS ET	https://doi.org/10.5061/dryad.9ghx3ffg0	Public	0	6	37
COS-7 cell overexpressing ER and mitochondria markers for CLEM	COS-7 Cell ER & Mitochondria FIB-SEM	https://doi.org/10.25378/janelia.13123385	Public	0	1	71
FIB-SEM Dataset (Obara + Nixon-Abell et al., 2023)	COS-7 Cell ER-Mitochondria Contact Site FIB-SEM	https://doi.org/10.25378/janelia.24502954.v1	Public	0	1	332
COS-7 Cell FIB-SEM Volume	COS-7 Cell FIB-SEM	https://doi.org/10.25378/janelia.24943716	Public	0	1	358
Interphase COS-7 Cell FIB-SEM Volume	COS-7 Cell FIB-SEM (Xu 2021)	https://doi.org/10.25378/janelia.24944559	Public	0	1	208
C. elegans motor circuit serial-section EM volumes	Caenorhabditis elegans Motor Circuit SEM	https://doi.org/10.60533/BOSS-2022-1JI1	Public	0	5	1592
Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network	Cal51 Cell Organelle Biogenesis Knockout FIB-SEM	https://doi.org/10.6019/EMPIAR-11695	Public	0	6	435
SBF-SEM datasets related to the manuscript "Trans-cellular tunnels induced by the fungal pathogen Candida albicans facilitate invasion through successive epithelial cells without host damage" by Lachat et al, 2022.	Candida albicans Epithelial Invasion SBF-SEM	https://doi.org/10.5281/zenodo.5776104	Public	0	11	450

657 datasets. Grouping: Public = external public repository; Outreach = contributed by an external laboratory through the outreach campaign; Internal = own group or close collaborators. Internal datasets are named as in their BioImage Archive depositions: treatment and condition labels are deliberately non-identifying, and the same label within one experiment denotes the same arm.

Citation

Acree et al., QuantEM: An optimized platform of vision transformer-based models for segmentation and analysis of electron microscopy data. Citation details on publication.

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