cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/tbrf4-hmk76
title: Xanthomonas vs Caulobac (-T1SS)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter (delta-cdzAB) competition. Caulobacter strain is a T1SS deletion strain.
description: <strong>Tilt Series Date:</strong> 2017-10-21</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the Xac strain, Caulobacter strain is from Laub lab. Data collected and processed by Mohammed Kaplan and Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-13/rawdata/</p>Xan_CaulDelT1_201721100012.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-13/rawdata/Xan_CaulDelT1_201721100012.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_201721100012_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_201721100012.ali,  356.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-13/file_25633/Xan_CaulDelT1_201721100012.ali"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_201721100012.tlt,  400.0 B  
        
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        Xan_CaulDelT1_201721100012_fid.tlt,  400.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.2pqzrp
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Miconia zubenetana"
 ]
}

 The dataset includes 65 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033096-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/pbnpv-k8v03
title: Xanthomonas vs minicells

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Ec-mini cells
description: <strong>Tilt Series Date:</strong> 2017-04-27</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-53.0°, 53.0°), step: 1.5°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the strains, data collected by Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Ec-mini cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot time= 10 sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-21/rawdata/</p>Xac-mini-20170427l30001.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-21/rawdata/Xac-mini-20170427l30001.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427l30001_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-21/3dimage_109213/Xac-mini-20170427l30001_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427l30001.ali,  477.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-21/file_26096/Xac-mini-20170427l30001.ali"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427l30001.tlt,  536.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-21/file_26097/Xac-mini-20170427l30001.tlt"
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        Xac-mini-20170427l30001_fid.tlt,  536.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16914400
title: Microstructure and Single-Pore Inertial Flow Dataset

description: Microstructure and Single-Pore Inertial Flow Dataset

[Kuldeep Singh]

August 2025

Overview

This dataset contains streamline and flow data from computational fluid dynamics (CFD) simulations of microstructure and single-pore geometries, used to study recirculation zones and non-Darcy flow in “Mechanism and Model of Flow-Dependent Inertial Permeability Resolves Forchheimer Theory” . It includes raw pressure-velocity data, processed  and eddy area data, COMSOL model files, and MATLAB analysis code. Streamline data for the microstructure are split into five files by pressure levels (105–190 Pa) due to their large size ( GB total), while single-pore streamline data are in a single file for testing.
DOI: 10.5281/zenodo.16914401
title: Microstructure and Single-Pore Inertial Flow Dataset

description: Microstructure and Single-Pore Inertial Flow Dataset

[Kuldeep Singh]

August 2025

Overview

This dataset contains streamline and flow data from computational fluid dynamics (CFD) simulations of microstructure and single-pore geometries, used to study recirculation zones and non-Darcy flow in “Mechanism and Model of Flow-Dependent Inertial Permeability Resolves Forchheimer Theory” . It includes raw pressure-velocity data, processed  and eddy area data, COMSOL model files, and MATLAB analysis code. Streamline data for the microstructure are split into five files by pressure levels (105–190 Pa) due to their large size ( GB total), while single-pore streamline data are in a single file for testing.
DOI: 10.22002/1hbbb-4nd87
title: Xanthomonas vs Caulobac (-T1SS)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter (delta-cdzAB) competition. Caulobacter strain is a T1SS deletion strain.
description: <strong>Tilt Series Date:</strong> 2017-10-21</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the Xac strain, Caulobacter strain is from Laub lab. Data collected and processed by Mohammed Kaplan and Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-8/rawdata/</p>Xan_CaulDelT1_201721100007.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-8/rawdata/Xan_CaulDelT1_201721100007.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_201721100007_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_201721100007.ali,  299.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-8/file_25693/Xan_CaulDelT1_201721100007.ali"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_201721100007.tlt,  336.0 B  
        
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        Xan_CaulDelT1_201721100007_fid.tlt,  336.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/anzdd-6b176
title: JV7967

description: Legionella thyA ΔdotI ΔdotJ
description: <strong>Tilt Series Date:</strong> 2016-08-11</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV7967 strain at OD~3.3. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-2/rawdata/</p>JV79670001.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-2/rawdata/JV79670001.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV79670001_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-2/3dimage_108431/JV79670001_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        JV79670001.tlt,  648.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-2/file_25190/JV79670001.tlt"
        > <i class="download icon"></i> Download </a></p>

        T2SSK.mod,  1.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-2/file_25191/T2SSK.mod"
        > <i class="download icon"></i> Download </a></p>

        T2SSK_2k.mod,  1.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-2/file_25192/T2SSK_2k.mod"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9a0jc-h6279
title: Xanthomonas vs minicells

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Ec-mini cells
description: <strong>Tilt Series Date:</strong> 2017-04-27</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-53.0°, 53.0°), step: 1.5°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the strains, data collected by Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Ec-mini cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot time= 10 sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-47/rawdata/</p>Xac-mini-20170427x20001.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-47/rawdata/Xac-mini-20170427x20001.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427x20001_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-47/3dimage_109253/Xac-mini-20170427x20001_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427x20001.ali,  506.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-47/file_26256/Xac-mini-20170427x20001.ali"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427x20001.tlt,  568.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-47/file_26257/Xac-mini-20170427x20001.tlt"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427x20001_fid.tlt,  568.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-47/file_26258/Xac-mini-20170427x20001_fid.tlt"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gtz4m-0t630
title: Xanthomonas vs Caulobac (-T1SS)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter (delta-cdzAB) competition. Caulobacter strain is a T1SS deletion strain.
description: <strong>Tilt Series Date:</strong> 2017-10-21</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the Xac strain, Caulobacter strain is from Laub lab. Data collected and processed by Mohammed Kaplan and Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-80/rawdata/</p>Xan_CaulDelT1_20172110f0016.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-80/rawdata/Xan_CaulDelT1_20172110f0016.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110f0016_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-80/3dimage_108818/Xan_CaulDelT1_20172110f0016_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110f0016.ali,  285.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-80/file_25696/Xan_CaulDelT1_20172110f0016.ali"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110f0016.tlt,  320.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-80/file_25697/Xan_CaulDelT1_20172110f0016.tlt"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110f0016_fid.tlt,  320.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-80/file_25698/Xan_CaulDelT1_20172110f0016_fid.tlt"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/d359d-cf617
title: JV7967

description: Legionella thyA ΔdotI ΔdotJ
description: <strong>Tilt Series Date:</strong> 2016-08-11</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV7967 strain at OD~3.3. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-16/rawdata/</p>JV79670008.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-16/rawdata/JV79670008.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV79670008_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        JV79670008.tlt,  648.0 B  
        
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        T2SSK.mod,  1.0 kB  
        
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        T2SSK_2k.mod,  1.0 kB  
        
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