cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/6wxgh-17r41
title: HIV gag session12 41KX

description: Opti-prep HIV gag shell
description: <strong>Tilt Series Date:</strong> 2009-04-13</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> HIV cores</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 2°, constant angular increment, dosage: 72.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Virgine; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Opti-prep</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-13-25/rawdata/</p>09apr13a_b19a_029.mrc,  Tilt Series (Pixel Size 0.512 nm), 570.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09apr13a_b19a_029_full.rec,  Reconstruction (Pixel Size 1.024 nm), 293.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/bvgqe-kbc70
title: Acetonema longum

description: A. longum grown on 1,2 Propanediol Day2
description: <strong>Tilt Series Date:</strong> 2011-05-30</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Eric Matson grew the cells</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown on 1,2 Propanediol</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-05-30-1/3dimage_25246/</p>1_full.rec,  Reconstruction (Pixel Size 1.9 nm), 396.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-05-30-1/3dimage_25246/1_full.rec"
        > <i class="download icon"></i> Download </a></p>

        target1.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/50hxa-5c070
title: Hyphomonas EB session21 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-07-14</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, EB 0.02mg/ml overnight 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
  jsa2009-07-14-55_slicer8730.jpg: Nucleoid  .  Hyphomonas neptunium
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-55/rawdata/</p>09jul14a_b200c_055.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        09jul14a_b200c_055_part.rec,  Reconstruction (Pixel Size 1.264 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/a00xz-gmt94
title: Acetonema longum grown on H2CO2

description: Raw data files of Acetonema longum grown on H2CO2
description: <strong>Tilt Series Date:</strong> 2009-03-11</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (60.0°, -60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Eric Matson grew the cells</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase in standard media </p>
<strong>Sample Preparation:</strong>  quantifoil grid, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-03-11-4/rawdata/</p>09mar11a_pos1Alongum_004.mrc,  Tilt Series (Pixel Size 0.961 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        cell4_full.rec,  Reconstruction (Pixel Size 1.922 nm), 335.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-03-11-4/3dimage_6403/cell4_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1fxka-frp38
title: MT310_xyl(+)_AuCl2uM(+)

description: Raw data files of MT310_xyl(+)_AuCl2uM(+)
description: <strong>Tilt Series Date:</strong> 2009-06-14</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> The MT310 strain was constructed by Martin Thanbichler; Cells cultured and treated by Zhuo Li; Data collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> MT310 cells were induced with xylose and treated with 2 uM CdCl2 for 20 hours.</p>
<strong>Sample Preparation:</strong> 10 nm gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-14-21/rawdata/</p>09jun14a_Cd2a_021.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun14a_Cd2a_021_full.rec,  Reconstruction (Pixel Size 1.9 nm), 471.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.xd23ej
title: Occurrence Download

description: A dataset containing 839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atoconeura kenya, Atoconeura, Atoconeura eudoxia, Atoconeura aethiopica, Atoconeura luxata, Atoconeura biordinata, Allocnemis cyanura, Allocnemis, Trithemis, Elattoneura villiersi, Elattoneura, Thermochoria equivocata, Thermochoria, Thermochoria jeanneli, Ischnura elegans, Ischnura, Selysiothemis nigra, Selysiothemis, Hemistigma affine, Hemistigma, Aciagrion, Sympetrum fonscolombii, Sympetrum, Micromacromia camerunica, Micromacromia, Micromacromia zygoptera, Aethiothemis erythromelas, Aethiothemis, Aciagrion gracile, Aciagrion dondoense, Trithetrum navasi, Trithetrum, Trithetrum congoense, Aciagrion africanum, Trithemis tropicana, Hadrothemis vrijdaghi, Hadrothemis, Hadrothemis scabrifrons, Hadrothemis defecta, Hadrothemis camarensis, Hadrothemis versuta, Hadrothemis infesta, Hadrothemis coacta, Hemicordulia, Diastatomma multilineatum, Diastatomma, Mastigogomphus chapini, Mastigogomphus, Crenigomphus kavangoensis, Crenigomphus, Pseudagrion merina, Pseudagrion, Allocnemis marshalli, Hemicordulia asiatica, Microgomphus, Cordulegaster boltonii algirica, Cordulegaster boltonii, Cordulegaster, Hemicordulia similis, Allocnemis elongata, Orthetrum malgassicum, Orthetrum, Lestinogomphus silkeae, Lestinogomphus, Hemicordulia virens, Microgomphus nyassicus, Paragomphus serrulatus, Paragomphus, Aeshna isoceles, Aeshna, Neurocordulia, Mortonagrion stygium, Mortonagrion, Pyrrhosoma nymphula, Pyrrhosoma, Proplatycnemis pseudalatipes, Proplatycnemis, Neophya rutherfordi, Neophya, Allocnemis superba, Elattoneura vittata, Onychogomphus nigrotibialis, Onychogomphus, Cordulia, Cordulia aenea, Stenocypha molindica, Stenocypha, Platycypha picta, Platycypha, Syncordulia venator, Syncordulia, Syncordulia gracilis, Crocothemis, Metacnemis valida, Metacnemis, Crocothemis sanguinolenta, Crocothemis erythraea, Platycypha rufitibia, Crocothemis saxicolor, Crocothemis striata)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((50.7597 -16.0878,50.8081 -15.9401,46.1382 -15.9401,46.1382 -24.9401,47.6434 -24.9401,49.8893 -18.4615,50.0065 -17.575,50.4326 -17.1196,50.4413 -16.4368,50.7597 -16.0878))"
 ]
}

 The dataset includes 839 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045745-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/s0f0f-yq963
title: Hyphomonas session14 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-05-22</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, overnight at 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-05-22-53/rawdata/</p>09may22b_bx22gr1_028.mrc,  Tilt Series (Pixel Size 0.774 nm), 520.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-05-22-53/rawdata/09may22b_bx22gr1_028.mrc"
        > <i class="download icon"></i> Download </a></p>

        09may22b_bx22gr1_028_1k.rec,  Reconstruction (Pixel Size 1.548 nm), 63.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/j0vp1-8cp35
title: MT310_xyl(+)_metal(-)

description: Raw data files of MT310_xyl(+)_metal(-)
description: <strong>Tilt Series Date:</strong> 2009-06-17</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> The MT310 strain was constructed by Martin Thanbichler. Cells were cultured and treated by Zhuo Li. Data were collected and processed by Zhuo.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> MT310 cells were induced with xylose for 20 hours. No metal salt was added. </p>
<strong>Sample Preparation:</strong> 10 nm gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-17-31/rawdata/</p>09jun17a_Ctnometal_036.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun17a_Ctnometal_036_full.rec,  Reconstruction (Pixel Size 1.9 nm), 471.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29986714.v1
title: Supplementary tables_CEAM

description: DNA methylation signatures are highly cell type-specific, yet most epigenome-wide association studies (EWAS) are performed on bulk tissue, potentially obscuring critical cell type-specific patterns. Existing computational tools for detecting cell type-specific DNAm changes are often limited by the accuracy of cell type deconvolution algorithms. Here, we introduce CEAM (Cell-type Enrichment Analysis for Methylation), a robust and interpretable framework for cell type enrichment analysis in DNA methylation data. CEAM applies over-representation analysis with cell type-specific CpG panels from Illumina EPIC arrays derived from nuclei-sorted cortical post-mortem brains from neurologically healthy aged individuals. The constructed CpG panels were systematically evaluated using both simulated datasets and published EWAS results from Alzheimer’s disease, Lewy body disease, and multiple sclerosis. CEAM demonstrated resilience to shifts in cell type composition, a common confounder in EWAS, and remained accurate across a wide range of differentially methylated positions, underscoring its flexibility. Application to existing EWAS findings generated in neurodegenerative diseases revealed enrichment patterns concordant with established disease biology, confirming CEAM’s biological relevance. The workflow is publicly available as an interactive Shiny app (https://um-dementia-systems-biology.shinyapps.io/CEAM/) enabling rapid, interpretable analysis of cell type-specific DNAm changes from bulk EWAS.
DOI: 10.22002/n09ff-h1960
title: CB15N w/ methanol control

description: Raw data files of CB15N w/ methanol control
description: <strong>Tilt Series Date:</strong> 2009-10-10</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Experiments done by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase in PYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1 or R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-10-49/rawdata/</p>09oct10b_WTCCmet_049.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        09oct10b_WTCCmet_049_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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DOI: 10.22002/wftnb-x1t81
title: Bsubtilis349

description: Bsubtilis JFG349 (MJ007, SpoIIIE78-11-GFP)
description: <strong>Tilt Series Date:</strong> 2011-08-08</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> JFG349, ponA null, SpoIIIE73-11-GFP</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from Kit Pogliano at UCSD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation media</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-08-08-34/3dimage_24892/</p>349_30005_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        349_30005.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-08-08-34/rawdata/349_30005.mrc"
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DOI: 10.22002/5r4dv-jg406
title: Eco 031910 MP49

description: Escherichia coli, 10mar24a_MP_49III_046,
description: <strong>Tilt Series Date:</strong> 2010-03-24</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 19.1 Martin</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-03-24-28/rawdata/</p>10mar24a_MP_49III_046.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        10mar24a_MP_49III_046_part.rec,  Reconstruction (Pixel Size 1.9 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.34740/kaggle/dsv/12872630
title: Daily Public Opinion on Israel-Palestine War
DOI: 10.22002/mm71e-m3p38
title: HUVECs CHMP4A+VPS4DN

description: HUVECs transfected with CHMP4A+VPS4DN constructs using Nucleofector Kit. Sample# C58-2
description: <strong>Tilt Series Date:</strong> 2010-12-13</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HUVECs</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> CHMP4A and VPS4DN construct provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2010-12-13-12/rawdata/</p>10dec13a_C45_4_016.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        10dec13a_C45_4_016_full.rec,  Reconstruction (Pixel Size 2.0 nm), 4.7 GB  
        
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