DOI: 10.22002/d1.20199
title: Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa

description: Raw and processed data and imaging files [0.42 TB total] for the bioRxiv preprint "Quantitative whole-tissue   3D imaging reveals bacteria in close association with mouse jejunum mucosa"
description: Related Publication:
Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa 

bioRxiv
eng
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/</p>DataSummary.xlsx,  14.7 kB  
        
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        Fig01-DataAnalysis-GrowthCurves.zip,  26.0 kB  
        
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        Fig01-DataAnalysis-RTqPCR.zip,  893.5 kB  
        
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        Fig02-DataAnalysis.zip,  287.5 kB  
        
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        Fig03-DataAnalysis.zip,  288.3 MB  
        
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        Fig04-Fig06-DataAnalysis.zip,  79.8 MB  
        
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        FigS07-DataAnalysis.zip,  316.7 MB  
        
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        FigS08-DataAnalysis.zip,  685.2 MB  
        
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        FigS09-DataAnalysis.zip,  245.5 MB  
        
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        FigS11-DataAnalysis.zip,  164.9 kB  
        
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        R4P-p091-20xC-ImarisSurfaceFiles.zip,  4.4 kB  
        
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        R4P-p091-D28C3M1-EJ-5x_Stitch.czi,  2.9 GB  
        
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        R4P-p091-D29C2M1-EJ-5x_Stitch.czi,  2.6 GB  
        
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        R4P-p091-D29C4M2-EJ-1.czi,  7.3 GB  
        
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        R4P-p091-D29C4M2-EJ-1.ims,  11.1 GB  
        
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        R4P-p091-D29C4M2-EJ-3.czi,  4.6 GB  
        
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        R4P-p091-D29C4M2-EJ-3.ims,  8.1 GB  
        
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        R4P-p091-D29C4M2-EJ-5x_Stitch.czi,  2.0 GB  
        
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        R4P-p091-D31C1M1-EJ-5x_Stitch.czi,  3.4 GB  
        
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        R4P-p121-Bfrag-v3EC-v3BAC-20x.czi,  1.5 GB  
        
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        R4P-p121-Ecoli-v3EC-v3BAC-20x.czi,  1.5 GB  
        
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        R4P-p124-20xC-ImarisSurfaceFiles.zip,  486.2 kB  
        
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        R4P-p124-D28C1M1-EJ-5x_Stitch.czi,  1.1 GB  
        
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        R4P-p124-D28C2M1-EJ-5x_Stitch.czi,  1.4 GB  
        
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        R4P-p124-D28C3M1-EJ-1.czi,  5.3 GB  
        
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        R4P-p124-D28C3M1-EJ-1.ims,  7.4 GB  
        
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        R4P-p124-D28C3M1-EJ-2.czi,  5.2 GB  
        
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        R4P-p124-D28C3M1-EJ-2.ims,  7.6 GB  
        
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        R4P-p124-D28C3M1-EJ-3.czi,  4.3 GB  
        
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        R4P-p124-D28C3M1-EJ-3.ims,  6.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D28C3M1-EJ-3.ims"
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        R4P-p124-D28C3M1-EJ-5x_Stitch.czi,  1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D28C3M1-EJ-5x_Stitch.czi"
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        R4P-p124-D28C4M1-EJ-1.czi,  4.8 GB  
        
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        R4P-p124-D28C4M1-EJ-1.ims,  9.7 GB  
        
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        R4P-p124-D28C4M1-EJ-2.czi,  4.8 GB  
        
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        R4P-p124-D28C4M1-EJ-2.ims,  7.0 GB  
        
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        R4P-p124-D28C4M1-EJ-3.czi,  4.1 GB  
        
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        R4P-p124-D28C4M1-EJ-3.ims,  6.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D28C4M1-EJ-3.ims"
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        R4P-p124-D28C4M1-EJ-4.czi,  5.0 GB  
        
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        R4P-p124-D28C4M1-EJ-4.ims,  7.4 GB  
        
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        R4P-p124-D28C4M1-EJ-5.czi,  5.7 GB  
        
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        R4P-p124-D28C4M1-EJ-5.ims,  8.9 GB  
        
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        R4P-p124-D28C4M1-EJ-5x_Stitch.czi,  1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D28C4M1-EJ-5x_Stitch.czi"
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        R4P-p124-D28C4M1-EJ-6.czi,  5.4 GB  
        
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        R4P-p124-D28C4M1-EJ-7.czi,  5.8 GB  
        
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        R4P-p124-D28C4M1-EJ-7.ims,  8.6 GB  
        
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        R4P-p124-D29C1M2-EJ-1.czi,  5.8 GB  
        
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        R4P-p124-D29C1M2-EJ-1.ims,  8.3 GB  
        
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        R4P-p124-D29C1M2-EJ-2.czi,  4.6 GB  
        
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        R4P-p124-D29C1M2-EJ-2.ims,  6.6 GB  
        
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        R4P-p124-D29C1M2-EJ-3.czi,  4.2 GB  
        
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        R4P-p124-D29C1M2-EJ-3.ims,  6.6 GB  
        
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        R4P-p124-D29C1M2-EJ-5x_Stitch.czi,  918.4 MB  
        
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        R4P-p124-D29C2M2-EJ-1.czi,  6.1 GB  
        
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        R4P-p124-D29C2M2-EJ-1.ims,  9.5 GB  
        
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        R4P-p124-D29C2M2-EJ-2.czi,  6.0 GB  
        
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        R4P-p124-D29C2M2-EJ-2.ims,  8.3 GB  
        
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        R4P-p124-D29C2M2-EJ-3.czi,  3.9 GB  
        
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        R4P-p124-D29C2M2-EJ-4.czi,  5.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D29C2M2-EJ-4.czi"
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        R4P-p124-D29C2M2-EJ-4.ims,  7.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D29C2M2-EJ-4.ims"
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        R4P-p124-D29C2M2-EJ-5x_Stitch.czi,  1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D29C2M2-EJ-5x_Stitch.czi"
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        R4P-p124-D29C3M2-EJ-5x_Stitch.czi,  1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D29C3M2-EJ-5x_Stitch.czi"
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        R4P-p124-D29C4M2-EJ-5x_Stitch.czi,  1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D29C4M2-EJ-5x_Stitch.czi"
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        R4P-p124-D30C1M3-EJ-5x_Stitch.czi,  877.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C1M3-EJ-5x_Stitch.czi"
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        R4P-p124-D30C2M3-EJ-1.czi,  3.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C2M3-EJ-1.czi"
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        R4P-p124-D30C2M3-EJ-1.ims,  5.9 GB  
        
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        R4P-p124-D30C2M3-EJ-2.czi,  4.4 GB  
        
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        R4P-p124-D30C2M3-EJ-2.ims,  8.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C2M3-EJ-2.ims"
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        R4P-p124-D30C2M3-EJ-3.czi,  4.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C2M3-EJ-3.czi"
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        R4P-p124-D30C2M3-EJ-3.ims,  6.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C2M3-EJ-3.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D30C2M3-EJ-5x_Stitch.czi,  1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C2M3-EJ-5x_Stitch.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D30C3M3-EJ-5x_Stitch.czi,  1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C3M3-EJ-5x_Stitch.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D30C4M3-EJ-5x_Stitch.czi,  1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D30C4M3-EJ-5x_Stitch.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C1M4-EJ-1.czi,  3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C1M4-EJ-1.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C1M4-EJ-1.ims,  5.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C1M4-EJ-1.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C1M4-EJ-2.czi,  3.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C1M4-EJ-2.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C1M4-EJ-2.ims,  5.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C1M4-EJ-2.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C1M4-EJ-3.czi,  6.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C1M4-EJ-3.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C1M4-EJ-3.ims,  8.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C1M4-EJ-3.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C1M4-EJ-5x_Stitch.czi,  949.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C1M4-EJ-5x_Stitch.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C2M4-JE-5x_Stitch.czi,  1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C2M4-JE-5x_Stitch.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-1.czi,  5.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-1.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-1.ims,  7.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-1.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-2.czi,  5.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-2.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-2.ims,  7.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-2.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-3.czi,  4.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-3.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-3.ims,  3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-3.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-4.czi,  5.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-4.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C3M4-EJ-5x_Stitch.czi,  1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C3M4-EJ-5x_Stitch.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-1.czi,  5.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-1.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-1.ims,  2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-1.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-2.czi,  4.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-2.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-2.ims,  6.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-2.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-3.czi,  5.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-3.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-4.czi,  5.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-4.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-4.ims,  8.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-4.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p124-D31C4M4-EJ-5x_Stitch.czi,  1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p124-D31C4M4-EJ-5x_Stitch.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p125-D31C4M4-CD455-WGA2-Crop.ims,  371.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p125-D31C4M4-CD455-WGA2-Crop.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p125-D31C4M4-CD455-WGA2.czi,  4.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p125-D31C4M4-CD455-WGA2.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p125-D31C4M4-CD455-WGA2.ims,  1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p125-D31C4M4-CD455-WGA2.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p125-D31C4M4-EpCAM5-WGA2-Crop.ims,  810.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p125-D31C4M4-EpCAM5-WGA2-Crop.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p125-D31C4M4-EpCAM5-WGA2.czi,  4.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p125-D31C4M4-EpCAM5-WGA2.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p125-D31C4M4-EpCAM5-WGA2.ims,  2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p125-D31C4M4-EpCAM5-WGA2.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p127-20xCS-ImarisSurfaceFiles.zip,  3.3 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p127-20xCS-ImarisSurfaceFiles.zip"
        > <i class="download icon"></i> Download </a></p>

        R4P-p127-D28C4M1-EJ-20xCS-1.czi,  8.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p127-D28C4M1-EJ-20xCS-1.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p127-D28C4M1-EJ-20xCS-1_Linear unmixing.czi,  1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p127-D28C4M1-EJ-20xCS-1_Linear unmixing.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p127-D28C4M1-EJ-20xCS-1_Linear unmixing.ims,  869.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p127-D28C4M1-EJ-20xCS-1_Linear unmixing.ims"
        > <i class="download icon"></i> Download </a></p>

        R4P-p127-D28C4M1-EJ-20xCS-2.czi,  8.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p127-D28C4M1-EJ-20xCS-2.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p127-D28C4M1-EJ-20xCS-2_Linear unmixing.czi,  1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p127-D28C4M1-EJ-20xCS-2_Linear unmixing.czi"
        > <i class="download icon"></i> Download </a></p>

        R4P-p127-D28C4M1-EJ-20xCS-2_Linear unmixing.ims,  824.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R4P-p127-D28C4M1-EJ-20xCS-2_Linear unmixing.ims"
        > <i class="download icon"></i> Download </a></p>

        R7P-p008-A4B8P0-A1B.01P4.czi,  651.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R7P-p008-A4B8P0-A1B.01P4.czi"
        > <i class="download icon"></i> Download </a></p>

        R7P-p008-A4B8P0-A4B0P4.czi,  789.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R7P-p008-A4B8P0-A4B0P4.czi"
        > <i class="download icon"></i> Download </a></p>

        R7P-p040-Ecoli-CFB560bV2-BacteroidesV3-20x.czi,  1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R7P-p040-Ecoli-CFB560bV2-BacteroidesV3-20x.czi"
        > <i class="download icon"></i> Download </a></p>

        R7P-p041-EUB338v2-UNIVv3-1.czi,  1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R7P-p041-EUB338v2-UNIVv3-1.czi"
        > <i class="download icon"></i> Download </a></p>

        R7P-p041-EUB338v2-UNIVv3-2.czi,  1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/0_D1.20199/R7P-p041-EUB338v2-UNIVv3-2.czi"
        > <i class="download icon"></i> Download </a></p>