cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/tvfpc-wh605
title: A22-treated wild type

description: Raw data files of A22-treated wild type
description: <strong>Tilt Series Date:</strong> 2009-07-21</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: 190.0 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> Cell culture and treatment by Zhuo Li. Data collected by Zhuo Li. Processed by Zhuo Li. </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponentially growing NA1000 cells were treated with 10 ug/ml A22 for 2 hours before freezing. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-21-6/rawdata/</p>09jul21a_A22wt_029.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul21a_A22wt_029_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/m04c8-nak71
title: Pdj 122708 634

description: Prosthecobacter dejongeii, 09jan04b_pdj_624w1_026,
description: <strong>Tilt Series Date:</strong> 2009-01-04</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</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: 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/mpa2009-01-04-13/rawdata/</p>09jan04b_pdj_624w1_026.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jan04b_pdj_624w1_026_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/f1vg0-4dg73
title: Alongum

description: Alongum_periplasmiclayers
description: <strong>Tilt Series Date:</strong> 2012-05-20</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: (-30.0°, 30.0°), 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> WesleyChen helped remove layers</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/etl2012-05-20-56/rawdata/</p>alongLys_20037.mrc,  Tilt Series (Pixel Size 0.95 nm), 512.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        alongLys_20038_full.rec,  Reconstruction (Pixel Size 1.95 nm), 309.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/k27qp-92p15
title: sporulating Bsubtilis MJ007

description: sporulating Bsubtilis MJ007, skinny Bacillus
description: <strong>Tilt Series Date:</strong> 2011-03-29</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> MJ007, ponA null</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> 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/etl2011-03-29-7/3dimage_25408/</p>11mar29a_gr4_008_part.rec,  Reconstruction (Pixel Size 1.9 nm), 943.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11mar29a_gr4_008.mrc,  Tilt Series (Pixel Size 0.95 nm), 947.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/2a662-sx233
title: Hyphomonas session16 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-06-06</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: (-61.0°, 61.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 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, 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
  jsa2009-06-06-25_slicer12902.jpg: Stalk
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-06-25/rawdata/</p>09jun06a_bx823c_001.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun06a_bx823c_001_full.rec,  Reconstruction (Pixel Size 1.548 nm), 419.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/a7r1k-1te30
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>
  jsa2009-05-22-63_slicer9064.jpg: intracellular budding vesicle, Hyphomonas neptunium
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-05-22-63/rawdata/</p>09may22b_bx22gr1_039.mrc,  Tilt Series (Pixel Size 0.774 nm), 520.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09may22b_bx22gr1_039_1k.rec,  Reconstruction (Pixel Size 1.548 nm), 120.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/zzyrw-x6149
title: Wild type control

description: Raw data files of Wild type control
description: <strong>Tilt Series Date:</strong> 2009-08-01</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: 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> RAPTOR, PEACH</p>
<strong>Collaborators and Roles:</strong> Experiments were done by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase NA1000 cells.</p>
<strong>Sample Preparation:</strong> 10 nm gold </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-11/rawdata/</p>09aug01a_noaddctl1_011.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09aug01a_noaddctl1_011_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4znxz-n4n22
title: Pdb 121509 MP35

description: Prosthecobacter debontii, 10feb07a_MP35_Pdb_exp_032,
description: <strong>Tilt Series Date:</strong> 2010-02-07</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter debontii</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: 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>
  mpa2010-02-07-7_slicer5778.jpg: Granules and vesicles mpa2010-02-07-7_slicer5780.jpg: Extracellular vesicle mpa2010-02-07-7_slicer5782.jpg: Pilli mpa2010-02-07-7_slicer5784.jpg: REZ
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-02-07-7/rawdata/</p>10feb07a_MP35_Pdb_exp_032.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb07a_MP35_Pdb_exp_032_part.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.nutaye
title: Occurrence Download

description: A dataset containing 21506 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.datasetkey = '24baf0da-60a9-4a13-99d7-a8c860c3cb30'
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 21506 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007074-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/8t7nr-8t679
title: MT-MreB treated w/ aurothiogluco

description: Raw data files of MT-MreB treated w/ aurothiogluco
description: <strong>Tilt Series Date:</strong> 2009-07-21</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: 190.0 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> Cell culture and treatment by Zhuo Li. Data collected by Zhuo Li. Processed by Zhuo Li. </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponentially growing MT310 cells were treated with 50 uM aurothioglucose for 20 hours before freezing. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-21-32/rawdata/</p>09jul21a_mtmrebaurothio1_019.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul21a_mtmrebaurothio1_019_part.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8jpyt-2bf91
title: B. subtilis 3267

description: Raw data files of B. subtilis 3267
description: <strong>Tilt Series Date:</strong> 2011-12-17</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> AD3267, ponA null, Alp7A-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>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Joe Pogliano</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow in LB</p>
<strong>Sample Preparation:</strong> Polara</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-17-15/rawdata/</p>32670015.mrc,  Tilt Series (Pixel Size 1.9 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        32670015_full.rec,  Reconstruction (Pixel Size 3.8 nm), 929.0 MB  
        
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DOI: 10.22002/kyvsa-ndn84
title: Hyphomonas session16 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-06-06</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: (-61.0°, 61.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 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 2216 media, 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/jsa2009-06-06-3/rawdata/</p>09jun06a_bx823a_024.mrc,  Tilt Series (Pixel Size 0.774 nm), 520.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun06a_bx823a_024_full.rec,  Reconstruction (Pixel Size 1.548 nm), 419.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/c8ws8-5jg79
title: Rhodobacter 1558 cryosections

description: Cryosections by MArk Ladinsky
description: <strong>Tilt Series Date:</strong> 2010-10-07</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 64.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in SUX media</p>
<strong>Sample Preparation:</strong> prepared for cryosectioning (gold prep see JWIKI)</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-10-07-10/rawdata/</p>10oct07a_rhcryosections_1_010.st,  Tilt Series (Pixel Size 0.0 nm), 528.5 MB  
        
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        10oct07a_rhcryosections_1_010.rec,  Reconstruction (Pixel Size 0.0 nm), 176.2 MB  
        
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