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a React WebGL-Based Tool
for Exploring Spatially Resolved
Single-Cell Transcriptomics Data
Jean Fan, PhD | Zhuang Lab | Bi...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 2
(Chen et al, Science 2015)
Gene A: 10...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 3
Image 1
Decoded barcode:
1
Simulated ...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 4
Image 2
Decoded barcode:
10
Simulated...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 5
Image 3
Decoded barcode:
101
Simulate...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 6
Decoded Data
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 7
Decoded Data
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 8
Decoded Data
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 9
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 10
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 11
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 12
big data demand scalable visualizati...
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Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 13
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Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 14
(courtesy of Nils Gehl...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 15
Uber visualizes people on a
geograph...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 16
MERmaid visualizes mRNAs
on Cartesia...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 17
csv file of positions and mRNA speci...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 18
Basic app offers:
• Highlighting up ...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 19
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Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 20
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Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 21
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Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 22
ADAM gene
expression per cell
à à
DA...
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Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 23
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 24
csv file of positions, cell-types,
a...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 25
Basic app
offers:
• Point size
optio...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 26
csv file of tSNE coordinates, cell-
...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 27
Basic app
offers:
• Point size
optio...
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 28
(courtesy of Nils Gehlenborg)•
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http://JEF.works
JEFworks
@JEFworks
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 29
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MERmaid - a React WebGL-Based Tool for Exploring Spatially Resolved Single-Cell Transcriptomics Data

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For Bio-IT World, Data Visualization & Exploration Tools 2019.

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MERmaid - a React WebGL-Based Tool for Exploring Spatially Resolved Single-Cell Transcriptomics Data

  1. 1. a React WebGL-Based Tool for Exploring Spatially Resolved Single-Cell Transcriptomics Data Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 1Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools
  2. 2. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 2 (Chen et al, Science 2015) Gene A: 101…0 Gene B: 110…1 … 100 to 1000s of targeted gene species (Wang et al, Nature Scientific Reports 2018)
  3. 3. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 3 Image 1 Decoded barcode: 1 Simulated Raw Data
  4. 4. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 4 Image 2 Decoded barcode: 10 Simulated Raw Data
  5. 5. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 5 Image 3 Decoded barcode: 101 Simulated Raw Data
  6. 6. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 6 Decoded Data
  7. 7. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 7 Decoded Data
  8. 8. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 8 Decoded Data
  9. 9. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 9
  10. 10. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 10
  11. 11. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 11
  12. 12. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 12 big data demand scalable visualization tools to assist in data exploration and hypothesis-generation
  13. 13. • • • • • Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 13
  14. 14. • • • • • • • Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 14 (courtesy of Nils Gehlenborg)
  15. 15. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 15 Uber visualizes people on a geographic coordinate map
  16. 16. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 16 MERmaid visualizes mRNAs on Cartesian coordinates
  17. 17. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 17 csv file of positions and mRNA species MERmaid app à
  18. 18. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 18 Basic app offers: • Highlighting up to 2 genes • Color picker option • Point size option Additional features: • Visualizing cell segmentation • Background image underlay (DAPI staining)
  19. 19. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 19 • •
  20. 20. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 20 • • • • • •
  21. 21. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 21 • • • • • •
  22. 22. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 22 ADAM gene expression per cell à à DAPI + poly-T staining Image segmentation
  23. 23. • • • • • • • Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 23
  24. 24. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 24 csv file of positions, cell-types, and gene expression MERmaid app (Moffittetal,Science2018)
  25. 25. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 25 Basic app offers: • Point size option • Coloring by gene expression • Restricting gene expression to specific cell- types
  26. 26. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 26 csv file of tSNE coordinates, cell- types, and gene expression MERmaid app
  27. 27. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 27 Basic app offers: • Point size option • Coloring by gene expression • Restricting gene expression to specific cell- types
  28. 28. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 28 (courtesy of Nils Gehlenborg)• • • • • • •
  29. 29. http://JEF.works JEFworks @JEFworks Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 29 Funding Find me online! Dulac Lab Catherine Dulac Dhananjay Bambah- Mukku jeanfan@fas.harvard.edu

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