cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.24085176
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse hippocampus (jrc_mus-hippocampus-1)

description: <b>Sample:</b> Hippocampus tissue from a wild-type, postnatal day 7 mouse, strain: C57BL/6J from Jackson Lab<b>Sample Description:</b> A dataset featuring isotropic 3D electron microscopy data of the mouse hippocampus (jrc_mus-hippocampus-1). The sample was obtained from a wild-type postnatal day 7 C57BL/6 mouse strain sourced from Jackson Laboratory. Mouse anesthesia was performed as IACUC guidelines. Perfusion fixation with glutaraldehyde and vibratome section. After low temperature reducing OTO staining, the sample was subject to dehydration, infiltration with graded ethanol and Durcupan resin, and polymerized in a 60°C oven. The sample was provided by Wei-Ping Li (HHMI/Janelia), prepared for imaging by Zhiyuan Lu (HHMI/Janelia), and imaged by Wei Qiu (HHMI/Janelia). Post-processing was conducted by Eric Trautman and Stephan Preibisch (HHMI/Janelia). This dataset offers a comprehensive view of a young mouse hippocampus cellular architecture.<b>Protocol:</b> Mouse anesthesia was performed as IACUC guidelines. Perfusion fixation with glutaraldehyde and vibratome section. After low temperature reducing OTO staining, the sample was subject to dehydration, infiltration with graded ethanol and Durcupan resin, and polymerized in a 60°C oven.<b>Contributions:</b> Sample provided by Wei-Ping Li (HHMI/Janelia), prepared for imaging by Zhiyuan Lu (HHMI/Janelia) and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID:</b> jrc_mus-hippocampus-1<b>Voxel size (nm):</b> 8 x 8 x 8 (x, y, z)<b>Data dimensions (µm): </b>141.38 x 142.63 x 196.38 (x, y, z)<b>Imaging start date:</b> 2023-07-21<b>Imaging duration (days):</b> 45<b>Scanning speed (MHz): </b>3<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_mus-hippocampus-1/jrc_mus-hippocampus-1.zarr/recon-1/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-hippocampus-1<b>Publication: </b>Xu et al., 2017<br>
DOI: 10.25378/janelia.24085176.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse hippocampus (jrc_mus-hippocampus-1)

description: <b>Sample:</b> Hippocampus tissue from a wild-type, postnatal day 7 mouse, strain: C57BL/6J from Jackson Lab<b>Sample Description:</b> A dataset featuring isotropic 3D electron microscopy data of the mouse hippocampus (jrc_mus-hippocampus-1). The sample was obtained from a wild-type postnatal day 7 C57BL/6 mouse strain sourced from Jackson Laboratory. Mouse anesthesia was performed as IACUC guidelines. Perfusion fixation with glutaraldehyde and vibratome section. After low temperature reducing OTO staining, the sample was subject to dehydration, infiltration with graded ethanol and Durcupan resin, and polymerized in a 60°C oven. The sample was provided by Wei-Ping Li (HHMI/Janelia), prepared for imaging by Zhiyuan Lu (HHMI/Janelia), and imaged by Wei Qiu (HHMI/Janelia). Post-processing was conducted by Eric Trautman and Stephan Preibisch (HHMI/Janelia). This dataset offers a comprehensive view of a young mouse hippocampus cellular architecture.<b>Protocol:</b> Mouse anesthesia was performed as IACUC guidelines. Perfusion fixation with glutaraldehyde and vibratome section. After low temperature reducing OTO staining, the sample was subject to dehydration, infiltration with graded ethanol and Durcupan resin, and polymerized in a 60°C oven.<b>Contributions:</b> Sample provided by Wei-Ping Li (HHMI/Janelia), prepared for imaging by Zhiyuan Lu (HHMI/Janelia) and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID:</b> jrc_mus-hippocampus-1<b>Voxel size (nm):</b> 8 x 8 x 8 (x, y, z)<b>Data dimensions (µm): </b>141.38 x 142.63 x 196.38 (x, y, z)<b>Imaging start date:</b> 2023-07-21<b>Imaging duration (days):</b> 45<b>Scanning speed (MHz): </b>3<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_mus-hippocampus-1/jrc_mus-hippocampus-1.zarr/recon-1/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-hippocampus-1<b>Publication: </b>Xu et al., 2017<br>
DOI: 10.5066/p1jrqp8u
title: Nest box colony field observations and avian egg tissue laboratory analyses from Lake Koocanusa and the Kootenai River Basin, Montana, 2022-2023

description: This data release includes nest box field observations (N = 98 nest boxes) and avian egg tissue laboratory analyses (N = 60 eggs) collected from Lake Koocanusa (also known as Koocanusa Reservoir) and the Kootenai River Basin, Montana, 2022-2023. Nest box field observation data (occupancy rate, clutch size, and hatching success) and avian eggs were collected by the U.S. Fish and Wildlife Service (USFWS) Montana Ecological Services Field Office (Helena, Montana), in cooperation with the University of Montana Bird Ecology Lab (Missoula, Montana), U.S. Army Corps of Engineers-Seattle District, Libby Dam-Kootenai River, (Libby, Montana), and U.S. Geological Survey (USGS) Wyoming-Montana Water Science Center (Helena, Montana). Preparation of egg tissue samples for metal(loid) analyses were conducted by the USFWS Montana Ecological Services Field Office and USFWS Mountain-Prairie Region (Lakewood, Colorado). Laboratory analyses [metal(loid)s] were conducted by the U.S. Environmental Protection Agency (USEPA), Region 10 Laboratory (Port Orchard, Washington). Specific metal(loid)s analyzed in avian egg tissue were arsenic (As), cadmium (Cd), copper (Cu), lead (Pb), manganese (Mn), nickel (Ni), selenium (Se), and zinc (Zn). This data release also compiles laboratory quality-assurance (QA) and quality-control (QC) data associated with the avian egg samples.
DOI: 10.25378/janelia.24222844
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse cerebellar granule neurons (jrc_mus-granule-neurons-1)

description: <b>Sample</b>: Cultured mouse cerebellar granule neurons transiently expressing HP1 mEmerald H3.3 SNAP (JF525) Lamin B Halo (JF646)<b>Sample Description</b>: Near isotropic FIB-SEM imaging of primary mouse granular neurons to study chromatin domains and their reorganization during development. Six cultured cells imaged in this dataset.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2%<b> </b>OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by David Solecki (St. Jude Children’s Research Hospital), prepared for imaging by Nirmala Iyer (HHMI/Janelia), with imaging by C. Shan Xu (Yale), and post-processing by Gleb Shtengel, and Harald Hess(HHMI/Janelia).<b>Acquisition ID</b>: jrc_mus-granule-neurons-1<b>Voxel size (nm)</b>: 4 x 4 x 3.76 (X, Y, Z)<b>Data dimensions (µm)</b>:<b> </b>52.0 x 5.4 x 16.4 (X, Y, Z)<b>Imaging start date</b>: 2018-04-27<b>Imaging duration (days)</b>: 11<b>Landing energy (eV)</b>: 1200<b>Imaging current (nA)</b>: 0.14<b>Scanning speed (MHz)</b>: 0.200<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-granule-neurons-1/jrc_mus-granule-neurons-1.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-granule-neurons-1<b>Publication</b>: Hoffman et al., 2020; Xu et al., 2017; Xu et al., 2021
DOI: 10.25378/janelia.24222844.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse cerebellar granule neurons (jrc_mus-granule-neurons-1)

description: <b>Sample</b>: Cultured mouse cerebellar granule neurons transiently expressing HP1 mEmerald H3.3 SNAP (JF525) Lamin B Halo (JF646)<b>Sample Description</b>: Near isotropic FIB-SEM imaging of primary mouse granular neurons to study chromatin domains and their reorganization during development. Six cultured cells imaged in this dataset.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2%<b> </b>OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by David Solecki (St. Jude Children’s Research Hospital), prepared for imaging by Nirmala Iyer (HHMI/Janelia), with imaging by C. Shan Xu (Yale), and post-processing by Gleb Shtengel, and Harald Hess(HHMI/Janelia).<b>Acquisition ID</b>: jrc_mus-granule-neurons-1<b>Voxel size (nm)</b>: 4 x 4 x 3.76 (X, Y, Z)<b>Data dimensions (µm)</b>:<b> </b>52.0 x 5.4 x 16.4 (X, Y, Z)<b>Imaging start date</b>: 2018-04-27<b>Imaging duration (days)</b>: 11<b>Landing energy (eV)</b>: 1200<b>Imaging current (nA)</b>: 0.14<b>Scanning speed (MHz)</b>: 0.200<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-granule-neurons-1/jrc_mus-granule-neurons-1.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-granule-neurons-1<b>Publication</b>: Hoffman et al., 2020; Xu et al., 2017; Xu et al., 2021
DOI: 10.15468/dl.eg3kb9
title: Occurrence Download

description: A dataset containing 7125 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sargassum horneri (Turner) C.Agardh, 1820"
 ]
}

 The dataset includes 7125 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020240-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ufppsx
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Columnea ferruginea J.F.Sm. & J.L.Clark"
 ]
}

 The dataset includes 15 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020241-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25378/janelia.24222868
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse cerebellar granule neurons (jrc_mus-granule-neurons-2)

description: <b>Sample</b>: Cultured mouse cerebellar granule neurons (progenitors) transiently expressing HP1 mEmerald / H3.3 SNAP (JF525) / Lamin B Halo(JF646)<b>Sample Description</b>: Near isotropic FIB-SEM imaging of primary mouse granular neurons to study chromatin domains and their reorganization during development. Six cultured cells imaged in this dataset.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2%<b> </b>OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by David Solecki (St. Jude Children’s Research Hospital), prepared for imaging by Nirmala Iyer (HHMI/Janelia), with imaging by C. Shan Xu (Yale), and post-processing by Gleb Shtengel, and Harald Hess(HHMI/Janelia).<b>Acquisition ID</b>: jrc_mus-granule-neurons-2<b>Voxel size (nm)</b>: 16 x 16 x 15.72 (X, Y, Z)<b>Data dimensions (µm)</b>:<b> </b>36.2 x 8.6 x 62 (X, Y, Z)<b>Imaging start date</b>: 2019-08-01<b>Imaging duration (days)</b>: 21<b>Landing energy (eV)</b>: 700<b>Imaging current (nA)</b>: 0.88<b>Scanning speed (MHz)</b>: 0.200<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-granule-neurons-2/jrc_mus-granule-neurons-2.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-granule-neurons-2<b>Publication</b>: Hoffman et al., 2020; Xu et al., 2017; Xu et al., 2021
DOI: 10.25378/janelia.24222868.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse cerebellar granule neurons (jrc_mus-granule-neurons-2)

description: <b>Sample</b>: Cultured mouse cerebellar granule neurons (progenitors) transiently expressing HP1 mEmerald / H3.3 SNAP (JF525) / Lamin B Halo(JF646)<b>Sample Description</b>: Near isotropic FIB-SEM imaging of primary mouse granular neurons to study chromatin domains and their reorganization during development. Six cultured cells imaged in this dataset.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2%<b> </b>OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by David Solecki (St. Jude Children’s Research Hospital), prepared for imaging by Nirmala Iyer (HHMI/Janelia), with imaging by C. Shan Xu (Yale), and post-processing by Gleb Shtengel, and Harald Hess(HHMI/Janelia).<b>Acquisition ID</b>: jrc_mus-granule-neurons-2<b>Voxel size (nm)</b>: 16 x 16 x 15.72 (X, Y, Z)<b>Data dimensions (µm)</b>:<b> </b>36.2 x 8.6 x 62 (X, Y, Z)<b>Imaging start date</b>: 2019-08-01<b>Imaging duration (days)</b>: 21<b>Landing energy (eV)</b>: 700<b>Imaging current (nA)</b>: 0.88<b>Scanning speed (MHz)</b>: 0.200<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-granule-neurons-2/jrc_mus-granule-neurons-2.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-granule-neurons-2<b>Publication</b>: Hoffman et al., 2020; Xu et al., 2017; Xu et al., 2021
DOI: 10.6084/m9.figshare.29236544
title: Supplementary dataset for "Heterologous plastoquinone production using a newly identified O2-dependent cyanobacterial hydroxylase", Dataset S1: PlqC HMM profile

description: This archive contains the PlqC protein profiles used to annotate the PlqC protein from the plastoquinone biosynthesis pathway.This is part of the Supplementary material of the study "Heterologous plastoquinone production using a newly identified O2-dependent cyanobacterial hydroxylase", submitted to <i>The FEBS</i><i> Journal</i>.Authors' list: Morgane Roger-Margueritat, Margot Beltran, Juliette Schnoebelen, Laura Flandrin, Wafa Rezali, Eline Michel, Sophie S. Abby, Fabien PierrelThe other HMM profiles used in this study were published in 10.1093/ismejo/wrae253 with the figshare link: https://doi.org/10.6084/m9.figshare.26390974
DOI: 10.6084/m9.figshare.29236544.v1
title: Supplementary dataset for "Heterologous plastoquinone production using a newly identified O2-dependent cyanobacterial hydroxylase", Dataset S1: PlqC HMM profile

description: This archive contains the PlqC protein profiles used to annotate the PlqC protein from the plastoquinone biosynthesis pathway.This is part of the Supplementary material of the study "Heterologous plastoquinone production using a newly identified O2-dependent cyanobacterial hydroxylase", submitted to <i>The FEBS</i><i> Journal</i>.Authors' list: Morgane Roger-Margueritat, Margot Beltran, Juliette Schnoebelen, Laura Flandrin, Wafa Rezali, Eline Michel, Sophie S. Abby, Fabien PierrelThe other HMM profiles used in this study were published in 10.1093/ismejo/wrae253 with the figshare link: https://doi.org/10.6084/m9.figshare.26390974
DOI: 10.5525/gla.researchdata.1988
title: Enforcement, extension, and entanglement: Punishing non-payment of financial penalties in Scotland - Community justice practitioner interviews

description: Interview transcripts with 9 community justice practitioners concerning their perspectives on the use, impact, and meaning of fines and financial penalties in Scotland.
DOI: 10.25378/janelia.24222892
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse cerebellar granule neurons (jrc_mus-granule-neurons-3)

description: <b>Sample</b>: Cultured mouse cerebellar granule neurons (progenitors) transiently expressing HP1 mEmerald / H3.3 SNAP (JF525) / Lamin B Halo(JF646)<b>Sample Description</b>: Near isotropic FIB-SEM imaging of primary mouse granular neurons to study chromatin domains and their reorganization during development. Six cultured cells imaged in this dataset.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2%<b> </b>OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by David Solecki (St. Jude Children’s Research Hospital), prepared for imaging by Nirmala Iyer (HHMI/Janelia), with imaging by C. Shan Xu (Yale), and post-processing by Gleb Shtengel, and Harald Hess(HHMI/Janelia).<b>Acquisition ID</b>: jrc_mus-granule-neurons-3<b>Voxel size (nm)</b>: 4 x 4 x 5.37 (X, Y, Z)<b>Data dimensions (µm)</b>:<b> </b>31.2 x 12.0 x 20.2 (X, Y, Z)<b>Imaging start date</b>: 2019-11-10<b>Imaging duration (days)</b>: 11<b>Landing energy (eV)</b>: 700<b>Imaging current (nA)</b>: 0.88<b>Scanning speed (MHz)</b>: 0.200<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-granule-neurons-3/jrc_mus-granule-neurons-3.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-granule-neurons-3<b>Publication</b>: Hoffman et al., 2020; Xu et al., 2017; Xu et al., 2021
DOI: 10.25378/janelia.24222892.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse cerebellar granule neurons (jrc_mus-granule-neurons-3)

description: <b>Sample</b>: Cultured mouse cerebellar granule neurons (progenitors) transiently expressing HP1 mEmerald / H3.3 SNAP (JF525) / Lamin B Halo(JF646)<b>Sample Description</b>: Near isotropic FIB-SEM imaging of primary mouse granular neurons to study chromatin domains and their reorganization during development. Six cultured cells imaged in this dataset.<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2%<b> </b>OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by David Solecki (St. Jude Children’s Research Hospital), prepared for imaging by Nirmala Iyer (HHMI/Janelia), with imaging by C. Shan Xu (Yale), and post-processing by Gleb Shtengel, and Harald Hess(HHMI/Janelia).<b>Acquisition ID</b>: jrc_mus-granule-neurons-3<b>Voxel size (nm)</b>: 4 x 4 x 5.37 (X, Y, Z)<b>Data dimensions (µm)</b>:<b> </b>31.2 x 12.0 x 20.2 (X, Y, Z)<b>Imaging start date</b>: 2019-11-10<b>Imaging duration (days)</b>: 11<b>Landing energy (eV)</b>: 700<b>Imaging current (nA)</b>: 0.88<b>Scanning speed (MHz)</b>: 0.200<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-granule-neurons-3/jrc_mus-granule-neurons-3.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-granule-neurons-3<b>Publication</b>: Hoffman et al., 2020; Xu et al., 2017; Xu et al., 2021
DOI: 10.15468/dl.mzhbpd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Lophuromys aquilus (True, 1892)",
 "RecordNumber is 5000",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020242-250525065834625/datasets/export for details.
DOI: 10.25378/janelia.24222652
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila brain: protocerebral bridge (jrc_fly-protocerebral-bridge)

description: <b>Sample:</b> Protocerebral bridge of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118)<b>Sample Description:</b> Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol:</b> Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.<b>Contributions:</b> Sample provided by Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (Yale), with post-processing by C. Shan Xu (Yale).<b>Acquisition ID:</b> jrc_fly-protocerebral-bridge<b>Voxel size (nm):</b> 4 x 4 x 2.68 (X, Y, Z)<b>Data dimensions (µm): </b>7.3 x 7.5 x 13.5 (X, Y, Z)<b>Imaging start date:</b> 2016-05-22<b>Imaging duration (days): </b>7<b>Landing energy (eV): </b>200<b>Imaging current (nA): </b>0.22<b>Scanning speed (MHz): </b>0.200<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_fly-protocerebral-bridge/jrc_fly-protocerebral-bridge.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_fly-protocerebral-bridge<b>Publication: </b>Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021<br>
DOI: 10.25378/janelia.24222652.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila brain: protocerebral bridge (jrc_fly-protocerebral-bridge)

description: <b>Sample:</b> Protocerebral bridge of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118)<b>Sample Description:</b> Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol:</b> Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.<b>Contributions:</b> Sample provided by Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (Yale), with post-processing by C. Shan Xu (Yale).<b>Acquisition ID:</b> jrc_fly-protocerebral-bridge<b>Voxel size (nm):</b> 4 x 4 x 2.68 (X, Y, Z)<b>Data dimensions (µm): </b>7.3 x 7.5 x 13.5 (X, Y, Z)<b>Imaging start date:</b> 2016-05-22<b>Imaging duration (days): </b>7<b>Landing energy (eV): </b>200<b>Imaging current (nA): </b>0.22<b>Scanning speed (MHz): </b>0.200<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_fly-protocerebral-bridge/jrc_fly-protocerebral-bridge.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_fly-protocerebral-bridge<b>Publication: </b>Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021<br>