`ili

`ili is a toolbox for 2D and 3D molecular mapping in Chrome.

`ili is developed by Alexandrov Team at EMBL Heidelberg.

• Developer: Sergey Ryazanov
• Principal investigator: Theodore Alexandrov

Hello bee

For a demonstration, open in Google Chrome

• 2D 3dmassomics visualisation example (a photo made during the 3D-MASSOMICS project meeting with simulated spots overlaid).
• 3D bee example (data provided by Yi Zeng from the Dorrestein Lab, UCSD).

Installation

There are 3 ways of running `ili in Chrome: from this website, using your http server, or as a Chrome App.

Input

`ili takes two files:

• PNG and CSV for 2D mapping (the format and examples to be added here soon)
• STL and CSV for 3D mapping (the format and examples to be added here soon)

How to use

`ili can be used for

• showing molecular maps (Ctrl/Cmd-up or -down)
• searching for a molecular map by the name substring by Ctrl-f
• adjusting visualizaiton of a map including colors, scaling, hotspot removal using quantile thresholding
• interactive visualization in 2D using mouse (zoom by wheeling, zoom into particular region by click-and-wheeling)
• interactive visualization in 3D using mouse (rotate by dragging, zoom by wheeling)
• saving the rendering as PNG by Ctrl-s (in Win/Lin) or Cmd-s (in Mac)

How to stay updated

Please sign up to the mailing list by sending an email to [email protected]

Miscellaneous

• **Why is it called ili?** ili in Hawaiian means skin and, among others, surface, area, or cover.
• How to record videos or screencasts in `ili? Please use a third-party software, for example ScreenCastify plugin to Chrome
• **How can I cite ili in my scientific publication?** We haven't published a paper devoted to \ili yet, so please cite Bouslimani et al. (2015) PNAS, our publication which motivated us the create and release `ili.

Funding acknowledgements

This project is funded from the European Union project 3D-MASSOMICS (FP7 HEALTH program, grant agreement no. 305259).