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

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. 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. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 3
Image 1
Decoded barcode:
1
Simulated Raw Data

4. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 4
Image 2
Decoded barcode:
10
Simulated Raw Data

5. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 5
Image 3
Decoded barcode:
101
Simulated Raw Data

6. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 6
Decoded Data

7. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 7
Decoded Data

8. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 8
Decoded Data

9. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 9

10. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 10

11. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 11

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. •
•
•
•
•
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 13

14. •
•
•
•
•
•
•
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 14
(courtesy of Nils Gehlenborg)

15. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 15
Uber visualizes people on a
geographic coordinate map

16. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 16
MERmaid visualizes mRNAs
on Cartesian coordinates

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. 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. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 19
•
•

20. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 20
•
•
•
•
•
•

21. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 21
•
•
•
•
•
•

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. •
•
•
•
•
•
•
Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 23

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. 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. 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. 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. Jean Fan, PhD | Zhuang Lab | Bio-IT World | Data Visualization & Exploration Tools 28
(courtesy of Nils Gehlenborg)•
•
•
•
•
•
•

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