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updated BBBC036 and BBBC037 (resolves #53 and #62) (#63)
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‎htdocs/BBBC036/BBBC036_v1_DatasetGroundTruth.csv

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/imaging/web/BBBC/high_throughput_images/BBBC036/BBBC036_v1_DatasetGroundTruth.csv

‎htdocs/BBBC036/index.html

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<h3>Images</h3>
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<p>Images are captured by ImageXpress Micro XLS automated microscope, with 5 fluorescent channels at x20 magnification, in 6 fields of view per well. Each image channel was then stored as a separate, grayscale image file in 16-bit TIF format.</p>
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<p><a href="https://idr.openmicroscopy.org/webclient/?show=screen-1751"><i class="icon-download-alt"></i> BBBC036 dataset </a></p>
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<p><a href="http://www.cellimagelibrary.org/pages/project_20269">BBBC036 dataset</a></p>
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<h3>Ground truth <a href="../benchmarking.html#bioLabel" class="badge" rel="tooltip" title="Biological labels">B</a></h3>
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<p>1553 compounds in the dataset are annotated with their known MoA(s), which are obtained from the repurposing hub (<a href="https://clue.io/repurposing-app">https://clue.io/repurposing-app</a>) (Corsello et al. 2017).</p>
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<p><a href="BBBC036_v1_DatasetGroundTruth.zip"><i class="icon-download-alt"></i> BBBC036_v1_DatasetGroundTruth.zip (130 KB)</a></p>
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<p><a href="BBBC036_v1_DatasetGroundTruth.zip"><i class="icon-download-alt"></i> BBBC036_v1_DatasetGroundTruth.csv (132 KB)</a></p>
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<h3>Metadata</h3>
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<p>Description of columns: </p>
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<ul>
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<li>Metadata_broad_sample: Internal Broad ID of the compound</li>

‎htdocs/BBBC037/BBBC037_v1_DatasetGroundTruth.csv

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/imaging/web/BBBC/high_throughput_images/BBBC037/BBBC037_v1_DatasetGroundTruth.csv

‎htdocs/BBBC037/index.html

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<h3>Images</h3>
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<p>Images from five fluorescent channels were captured at 20x magnification on an ImageXpress Micro epifluorescent microscope (Molecular Devices). Nine sites per well were acquired, with laser based autofocus using the DAPI channel at the first site of each well. Each image channel was then stored as a separate, grayscale image file in 16-bit TIF format.</p>
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<p><a href="BBBC037_v1_dataset.zip"><i class="icon-download-alt"></i> BBBC037_v1_dataset.zip (7 KB)</a></p>
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<p><a href="https://idr.openmicroscopy.org/webclient/?show=screen-1751">BBBC037 dataset</a></p>
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<h3>Ground truth <a href="../benchmarking.html#bioLabel" class="badge" rel="tooltip" title="Biological labels">B</a></h3>
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<p>Each gene is annotated with its biological pathway, generated by domain experts at our institution. </p>
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<p><a href="BBBC037_v1_DatasetGroundTruth.zip"><i class="icon-download-alt"></i> BBBC037_v1_DatasetGroundTruth.zip (150.9 MB)</a></p>
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<p><a href="BBBC037_v1_DatasetGroundTruth.csv"><i class="icon-download-alt"></i> BBBC037_v1_DatasetGroundTruth.csv (8 KB)</a></p>
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<h3>Metadata</h3>
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<p>Description of columns: </p>
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<p>
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<ul>
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<li>Gene Allele Name: Gene and allele symbols</li>
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</ul>
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</p>
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<p>Pathway annotations are generated by domain experts at the Broad Institute. </p>
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<h3>For more information</h3>
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<p>These images were contributed by Mark Bray. More information about this dataset can be found in the publication below (<a href="http://dx.doi.org/10.1038/nmeth.2083">Rohban, 2017</a>).</p>
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<p>More information about this dataset can be found in the publication below (<a href="http://dx.doi.org/10.1038/nmeth.2083">Rohban, 2017</a>).</p>
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<h3>Published results using this image set</h3>
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<p>Rohban, Mohammad Hossein, Shantanu Singh, Xiaoyun Wu, Julia B. Berthet, Mark-Anthony Bray, Yashaswi Shrestha, Xaralabos Varelas, Jesse S. Boehm, and Anne E. Carpenter (2017). Systematic Morphological Profiling of Human Gene and Allele Function via Cell Painting. eLife 6 (March). <a href="https://doi.org/10.7554/eLife.24060">10.7554/eLife.24060</a>. PMID: 28315521 PMCID: PMC5386591</p>
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[<a href="http://dx.doi.org/10.1038/nmeth.2083">Ljosa et al., <i>Nature Methods</i>, 2012</a>].&quot;</p>
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<h3>Copyright</h3>
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<p><a rel="license" href="http://creativecommons.org/licenses/by/3.0/">
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<img alt="Creative Commons License" style="border-width:0" src="http://i.creativecommons.org/l/by/3.0/88x31.png" />
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</a> These images are licensed under a
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<a rel="license" href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported License</a>
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by <span xmlns:cc="http://creativecommons.org/ns#" property="cc:attributionName"><a href="mailto:[email protected]">Mohammad Rohban</a></span>. </p>
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<p><a href="http://creativecommons.org/publicdomain/zero/1.0/" rel="license"><img alt="CC0" src="http://i.creativecommons.org/p/zero/1.0/88x31.png" style="border-style: none;"></a> Copyright: CC0. To the extent possible under law, <a href="mailto:[email protected]">Jesse Boehm</a> has waived all copyright and related or neighboring rights to <span property="dct:title">BBBC037v1</span>.</p>
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<footer class="footer">
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<p>This page last updated 2018-05-17</p>

‎templates/BBBC036.html

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<h3>Images</h3>
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<p>Images are captured by ImageXpress Micro XLS automated microscope, with 5 fluorescent channels at x20 magnification, in 6 fields of view per well. Each image channel was then stored as a separate, grayscale image file in 16-bit TIF format.</p>
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<p><a href="https://idr.openmicroscopy.org/webclient/?show=screen-1751"><i class="icon-download-alt"></i> BBBC036 dataset </a></p>
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<p><a href="http://www.cellimagelibrary.org/pages/project_20269">BBBC036 dataset</a></p>
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<h3>Ground truth {{B}}</h3>
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<p>1553 compounds in the dataset are annotated with their known MoA(s), which are obtained from the repurposing hub (<a href="https://clue.io/repurposing-app">https://clue.io/repurposing-app</a>) (Corsello et al. 2017).</p>
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<p><a href="BBBC036_v1_DatasetGroundTruth.zip"><i class="icon-download-alt"></i> BBBC036_v1_DatasetGroundTruth.zip (130 KB)</a></p>
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<p><a href="BBBC036_v1_DatasetGroundTruth.zip"><i class="icon-download-alt"></i> BBBC036_v1_DatasetGroundTruth.csv (132 KB)</a></p>
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<h3>Metadata</h3>
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<p>Description of columns: </p>
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<ul>
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<li>Metadata_broad_sample: Internal Broad ID of the compound</li>

‎templates/BBBC037.html

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<h3>Images</h3>
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<p>Images from five fluorescent channels were captured at 20x magnification on an ImageXpress Micro epifluorescent microscope (Molecular Devices). Nine sites per well were acquired, with laser based autofocus using the DAPI channel at the first site of each well. Each image channel was then stored as a separate, grayscale image file in 16-bit TIF format.</p>
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<p><a href="BBBC037_v1_dataset.zip"><i class="icon-download-alt"></i> BBBC037_v1_dataset.zip (7 KB)</a></p>
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<p><a href="https://idr.openmicroscopy.org/webclient/?show=screen-1751">BBBC037 dataset</a></p>
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<h3>Ground truth {{B}}</h3>
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<p>Each gene is annotated with its biological pathway, generated by domain experts at our institution. </p>
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<p><a href="BBBC037_v1_DatasetGroundTruth.zip"><i class="icon-download-alt"></i> BBBC037_v1_DatasetGroundTruth.zip (150.9 MB)</a></p>
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<p><a href="BBBC037_v1_DatasetGroundTruth.csv"><i class="icon-download-alt"></i> BBBC037_v1_DatasetGroundTruth.csv (8 KB)</a></p>
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<h3>Metadata</h3>
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<p>Description of columns: </p>
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<p>
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<ul>
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<li>Gene Allele Name: Gene and allele symbols</li>
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</ul>
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</p>
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<p>Pathway annotations are generated by domain experts at the Broad Institute. </p>
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<h3>For more information</h3>
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<p>These images were contributed by Mark Bray. More information about this dataset can be found in the publication below (<a href="http://dx.doi.org/10.1038/nmeth.2083">Rohban, 2017</a>).</p>
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<p>More information about this dataset can be found in the publication below (<a href="http://dx.doi.org/10.1038/nmeth.2083">Rohban, 2017</a>).</p>
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<h3>Published results using this image set</h3>
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<p>Rohban, Mohammad Hossein, Shantanu Singh, Xiaoyun Wu, Julia B. Berthet, Mark-Anthony Bray, Yashaswi Shrestha, Xaralabos Varelas, Jesse S. Boehm, and Anne E. Carpenter (2017). Systematic Morphological Profiling of Human Gene and Allele Function via Cell Painting. eLife 6 (March). <a href="https://doi.org/10.7554/eLife.24060">10.7554/eLife.24060</a>. PMID: 28315521 PMCID: PMC5386591</p>
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[<a href="http://dx.doi.org/10.1038/nmeth.2083">Ljosa et al., <i>Nature Methods</i>, 2012</a>].&quot;</p>
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<h3>Copyright</h3>
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<p><a rel="license" href="http://creativecommons.org/licenses/by/3.0/">
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<img alt="Creative Commons License" style="border-width:0" src="http://i.creativecommons.org/l/by/3.0/88x31.png" />
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</a> These images are licensed under a
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<a rel="license" href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported License</a>
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by <span xmlns:cc="http://creativecommons.org/ns#" property="cc:attributionName"><a href="mailto:[email protected]">Mohammad Rohban</a></span>. </p>
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<p><a href="http://creativecommons.org/publicdomain/zero/1.0/" rel="license"><img alt="CC0" src="http://i.creativecommons.org/p/zero/1.0/88x31.png" style="border-style: none;"></a> Copyright: CC0. To the extent possible under law, <a href="mailto:[email protected]">Jesse Boehm</a> has waived all copyright and related or neighboring rights to <span property="dct:title">{{acc}}v1</span>.</p>
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<footer class="footer">
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<p>This page last updated 2018-05-17</p>

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