Cell Viewer

User Interface for Cell Universe

Usage

Using Sample Data

For only viewing, can open at https://celluniverse.github.io/cellviewer/#/.

For local copy:

• Requirements: npm
• Download/clone files from simmaneal folder
• cd into cellviewer
• Run npm install
• Use npm start and open localhost:3000

Using Your Own Data

• Requirements: Python3.7, svgwrite (installable from pip)
• Download/clone files from simmaneal folder
• Run simmaneal main.py code (Check Simmaneal Documentation for more info)
• Move the output folder into cellviewer
• cd into cellviewer
• Run python3.7 radialtree.py [output] where [output] is your output directory that you just moved, without brackets
• Drag and drop your [output] folder to the file dropzone on the website

Assumptions

• simmaneal produce an output folder that contains at least:
  • colony.csv
    • with headers: frame,name,x,y,width,length,rotation
    • sorted in ascending order according to frame number
    • each cell's name starts with a 'b'
    • each cell's children (when it splits) is name+'0' and name+'1'
  • images for each frame
    • same dimensions

Limitations

• Colors are limited (4)
• Not tested with other versions of Python
• Browsers tested : Chrome, Safari, FireFox
• Browsers failed : Edge
• Bad mobile compatibility
• Lag in more dense frames

To Do

• Add color picker
• Raw Image Files
• Optimize
  • Original Image Size should be obtained quicker, assume same dimension for each frame
• Pipeline from simmanneal