`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); zoom out by using the mosue wheel to see the full image and follow instructions.
• 3D bee example (data provided by Yi Zeng from the Dorrestein Lab, UCSD); follow instructions.

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:

• for 2D mapping: a PNG to be used as the background image (example), and a CSV with intensities and coordinates (example)
• for 3D mapping: a binary STL of the 3D model (example), and a CSV with intensities and coordinates (example)

What is `ili for?

Among other things, `ili can be used for

• showing molecular maps (Ctrl-up or -down in Win/Lin; Cmd-up or Cmd-down in Mac)
• searching for a molecular map by a name substring (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)
• showing the name of a spot by clicking at it
• 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 ili-toolbox+subscribe@googlegroups.com

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

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