Imaris File Parsers for NIH

Update:

Project Description

• This repo is designed to extract statistical information from raw Imaris file with (.ims) extension.
• This script does not calculate any statistical information, it simply extracts existing information from each .ims file and formats in a manner that helps with downsteam stream analysis software such as FlowJo.

Setup

• Tested on: Windows 10, Ubuntu 20.04
• Install Time: <10 minutes Create Enviroment:

conda env create -f environment.yml

Usage Tips

• We currently offer 4 types of data parsers
  • Surface Stats
  • Surface Track Stats
  • Surfaces at Unique Time Steps
  • All Tracks
• Each of the jupyter notebooks for the parsers above uses a config file from parsers/config/ folder.
• To extract information from your own Imaris Files, simply grab the paths to each directory that contains the .ims files and update the config.yaml file, provide a save directory and run any one of the notebooks to extract the relevant information.
• For each file a formatted csv file will be generated that contains all relevant statistical information from each .ims file for further analysis.

Folder Structure

• Parsers
  • data
  • parsers
    • config
    • imaris
    • parsers
    • scripts
    • utils

Contributors

• Shehan Perera
• Juraj Kabat