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Single Cell Multiplexed Imaging Jupyter Voila Dashboard using CODEX Data
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original-index.ipynb first commit of codex_dashboard Jul 31, 2019
requirements.txt Update to latest voila Aug 5, 2019

CODEX Single Cell Multiplexed Imaging Dashboard



Goltsev et al used a highly multiplexed cytometric approach called CODEX to measure ~30 surface markers in spatially resolved single cells from mouse spleens. We utilized Clustergrammer2 to hierarchically cluster ~5,000 sinlge cells (from a subset of a segmented spleen image). We also used the Jupyter Widget bqplot to visualize single cell location data using voronoi plots. We then built a dasnboard using the library voila, which converts Jupyter notebooks to dashboards/web-apps, and linked our heatmap to the spatial map. This allows to interact with the Clustergrammer2 heatmap and highlight cells in the spatially resolved map. These kind of linked views are crucial for exploration of spatially resolved high-dimensional single cell data. Finally, we are running this dashboard using MyBinder.

YouTube Tutorial


CODEX data from:

Voila dashboard example originally from:

Note: works best in Chrome Browser.

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