cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/b6n45-hke33
title: Acidovorax

description: Acidovorax grown in NB
description: <strong>Tilt Series Date:</strong> 2009-04-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acidovorax sp.</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 0.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> grown by Bill Hickey at UW-Madison; data collected and processed by Elitza Tocheva</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in NB.</p>
<strong>Sample Preparation:</strong> 20nm gold, 2s blot, -2 offset</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-04-01-20/rawdata/</p>09mar31a_v_021.mrc,  Tilt Series (Pixel Size 0.962 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-04-01-20/rawdata/09mar31a_v_021.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/z6f6v-ymz41
title: Agro_C58_22C_liq

description: Raw data files of Agro_C58_22C_liq
description: <strong>Tilt Series Date:</strong> 2014-09-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, 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> strain from Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 22C liquid</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-09-05-7/rawdata/</p>22_liq_c580002.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qdzem-g1k70
title: Hyphomonas session9 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-07</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: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 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...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-65/rawdata/</p>09mar07a_36c_068.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-65/rawdata/09mar07a_36c_068.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/anacc-s7t55
title: Hyphomonas session10 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-28</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: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -8.0 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...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-28-24/rawdata/</p>09mar28a_bx60c_025.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/q8qgn-5eg11
title: Agrobacterium tumefaciens

description: Agro VG3101
description: <strong>Tilt Series Date:</strong> 2013-10-31</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, 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> AutoPatch</p>
<strong>Collaborators and Roles:</strong> Elliot Meyerwitz</p>
<strong>Purification / Growth Conditions / Treatment:</strong> liquid LB+antibiotics</p>
<strong>Sample Preparation:</strong> Vitrobot blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-10-31-31/rawdata/</p>agro_vg31010018.mrc,  Tilt Series (Pixel Size 0.4 nm), 3.4 GB  
        
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DOI: 10.22002/msfeh-3na96
title: Hyphomonas session8 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-06</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: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 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...</p>
<strong>Sample Preparation:</strong> C-flat grid, 5nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-06-48/rawdata/</p>09mar06a_20d_048.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ksz6s-ctx98
title: Acidovorax

description: Acidovorax grown in NB
description: <strong>Tilt Series Date:</strong> 2009-04-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acidovorax sp.</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 0.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> grown by Bill Hickey at UW-Madison; data collected and processed by Elitza Tocheva</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in NB.</p>
<strong>Sample Preparation:</strong> 20nm gold, 2s blot, -2 offset</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-04-01-27/rawdata/</p>09mar31a_v_029.mrc,  Tilt Series (Pixel Size 0.962 nm), 1.0 GB  
        
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DOI: 10.22002/n6tgz-95771
title: Hyphomonas session10 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-28</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: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -8.0 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...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-28-45/rawdata/</p>09mar28a_bx60c_046.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-28-45/rawdata/09mar28a_bx60c_046.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.pdrwnu
title: Occurrence Download

description: A dataset containing 191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Percina nevisense)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 191 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013758-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/rqa7z-xwd71
title: Acetonema longum

description: Sacculi of sporulating A. longum
description: <strong>Tilt Series Date:</strong> 2010-12-07</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> cells grown by Eric Matson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> anaerobic</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/etl2010-12-07-14/rawdata/</p>10dec07a_grid5Sac_047.mrc,  Tilt Series (Pixel Size 0.95 nm), 788.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/z3df4-tpm90
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/zla2009-10-10-14/rawdata/</p>09oct10b_WTCCmet_014.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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DOI: 10.22002/w45nw-p5s96
title: IST1 N-terminal

description: IST1 N-terminal
description: <strong>Tilt Series Date:</strong> 2009-11-11</p>
<strong>Data Taken By:</strong> Megan Dobro</p>
<strong>Species / Specimen:</strong> IST1N tubes</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 1.0 eV/Å²,  defocus: -3.5 μm,  magnification: 41000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> purified by John McCullough, University of Utah</p>
<strong>Purification / Growth Conditions / Treatment:</strong> dialysis step upon receiving protein</p>
<strong>Sample Preparation:</strong> Vitrobot, varying blot times and offset, 100% humidity, 22 C, 10 nm gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2009-11-11-9/rawdata/</p>09nov11b_Box380grid2_010.mrc,  Tilt Series (Pixel Size 0.51 nm), 520.1 MB  
        
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DOI: 10.5281/zenodo.17008869
title: MSCA TaphArt Project -  Images and 3D models of experimental samples

description: Data produced in the framework of the MSCA project “TaphArt: exploring the potential existence of rock art paintings in the Middle Stone Age of southern Africa and its destruction due to the action of taphonomic processes” (Grant Agreement No. 101109977, EC signature date: 7 April 2023; start date: 1 September 2023; end date: 31 August 2025). The project has received funding from the European Union’s Horizon Europe research and innovation programme under the Marie Skłodowska-Curie Actions (MSCA).

The project investigates the absence of Middle Stone Age rock art in southern Africa—specifically at Blombos Cave—and whether this absence is the result of taphonomic processes rather than cultural choices. It adopts an innovative, interdisciplinary approach that integrates archaeology, paleoenvironmental science, atmospheric science, material science, and analytical chemistry.

This dataset brings together two complementary collections of experimental documentation:





Images of experimental samples: high-resolution microscope images (.jpg) acquired with a Hirox HRX-01 3D Digital Microscope at the Institute of Solar Research, German Aerospace Center (DLR). Each experimental sample measures 5 × 5 cm and contains eight 1 × 1 cm painted panels prepared with different pictorial recipes (water + blood, water + ochre, water + milk, water + marrow, water + egg, water + fat, water + saliva, water + sap). Images were captured in three states: PRE (before accelerated ageing), POST1 (after the first ageing cycle), and POST2 (after the second ageing cycle).




3D models of experimental samples: surface models (.tdr format) of the same samples, also acquired with the Hirox HRX-01 microscope at magnifications of 20× and 40×. These models document the state of the surfaces in PRE, POST1, and POST2 conditions, providing quantitative and qualitative information about degradation processes.



Together, these sub-datasets provide both 2D high-resolution images and 3D digital surface models. They serve as scientific documentation of the experimental workflow and as reusable digital resources supporting reproducibility, transparency, and future research on the taphonomy and preservation of rock art.
DOI: 10.5281/zenodo.17008870
title: MSCA TaphArt Project -  Images and 3D models of experimental samples

description: Data produced in the framework of the MSCA project “TaphArt: exploring the potential existence of rock art paintings in the Middle Stone Age of southern Africa and its destruction due to the action of taphonomic processes” (Grant Agreement No. 101109977, EC signature date: 7 April 2023; start date: 1 September 2023; end date: 31 August 2025). The project has received funding from the European Union’s Horizon Europe research and innovation programme under the Marie Skłodowska-Curie Actions (MSCA).

The project investigates the absence of Middle Stone Age rock art in southern Africa—specifically at Blombos Cave—and whether this absence is the result of taphonomic processes rather than cultural choices. It adopts an innovative, interdisciplinary approach that integrates archaeology, paleoenvironmental science, atmospheric science, material science, and analytical chemistry.

This dataset brings together two complementary collections of experimental documentation:





Images of experimental samples: high-resolution microscope images (.jpg) acquired with a Hirox HRX-01 3D Digital Microscope at the Institute of Solar Research, German Aerospace Center (DLR). Each experimental sample measures 5 × 5 cm and contains eight 1 × 1 cm painted panels prepared with different pictorial recipes (water + blood, water + ochre, water + milk, water + marrow, water + egg, water + fat, water + saliva, water + sap). Images were captured in three states: PRE (before accelerated ageing), POST1 (after the first ageing cycle), and POST2 (after the second ageing cycle).




3D models of experimental samples: surface models (.tdr format) of the same samples, also acquired with the Hirox HRX-01 microscope at magnifications of 20× and 40×. These models document the state of the surfaces in PRE, POST1, and POST2 conditions, providing quantitative and qualitative information about degradation processes.



Together, these sub-datasets provide both 2D high-resolution images and 3D digital surface models. They serve as scientific documentation of the experimental workflow and as reusable digital resources supporting reproducibility, transparency, and future research on the taphonomy and preservation of rock art.
DOI: 10.22002/z437q-sqy70
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/jsa2009-04-13-19/rawdata/</p>09apr13a_b19a_020.mrc,  Tilt Series (Pixel Size 0.512 nm), 570.4 MB  
        
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DOI: 10.22002/719jt-5zs25
title: MamJ deletion w/o iron

description: No magnetosome vesicles, suspected as a mutant that has lost the magnetosome island
description: <strong>Tilt Series Date:</strong> 2010-01-22</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Magnetospirillum magneticum</p>
<strong>Strain:</strong> AMB-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -16.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> Raptor and Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Mutant constructed by Arash Komeili, cells shipped to and imaged by Zhuo Li</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Stationary phase</p>
<strong>Sample Preparation:</strong> Quantifoid grid, 10-nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-01-22-7/rawdata/</p>10jan22a_dJnofe2_010.mrc,  Tilt Series (Pixel Size 0.0 nm), 1.0 GB  
        
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