Gravity Machine Analysis GUI

Introduction

This is a custom GUI-based data analysis tool for visualizing and analyzing Gravity Machine datasets. Gravity machine a.k.a Scale-free Vertical Tracking Microscopy, a method developed by Deepak Krishnamurthy et al. at Prakash lab, Stanford.

The dependencies can be installed by following instructions in the GM_Analysis_Installation.md file.

To launch the tool, open a terminal, activate the appropriate virtual environment (conda activate ...). After this launch the folowing script:

python DataAnalyser.py

Basic usage

[IMPORTANT] Data specific configuration

Since different datasets may save different fields. Use an existing 'configuration_*.txt' file found in the configurations or folder or create a new one based on the data fields saved in your datasets. The configuration file specifies how these datafields are mapped to the internal variables used within the data-viewer.

Opening a dataset

To open a new dataset, hit 'Ctrl + O' or click File > Open. Then first choose the folder containing the data (.csv track file + folder containing images). In the next dialog, choose the .csv track file you wish to open.

Changing track parameters

To change track parameters such as Pixel size, chamber dimensions etc., navigate to Edit > Track parameters or hit 'Ctrl + T'.

Changing Video Playback speed

To change the playback speed of the video, navigate to Video > Video Parameters or hit 'Ctrl + V'. Use the slider or entry box to enter the playback factor. Playback factor of '1' corresponds to real-time playback.

Saving analysis data

Currently a very basic widget allows you to annotate the track ID, condition and also choose the time interval of interest. This widget also allows a simple means to stimate the size of the tracked object. This analysis notes can be saved as a CSV file by clicking 'Save analysis params'.

Publications:

1. Krishnamurthy, Deepak, Hongquan Li, François Benoit du Rey, Pierre Cambournac, Adam G. Larson, Ethan Li, and Manu Prakash. "Scale-free vertical tracking microscopy." Nature Methods (2020): 1-12. Weblink

To cite this tool

@article{krishnamurthy2020scale,
  title={Scale-free vertical tracking microscopy},
  author={Krishnamurthy, Deepak and Li, Hongquan and du Rey, Fran{\c{c}}ois Benoit and Cambournac, Pierre and Larson, Adam G and Li, Ethan and Prakash, Manu},
  journal={Nature Methods},
  volume={17},
  number={10},
  pages={1040--1051},
  year={2020},
  publisher={Nature Publishing Group}
}

Contributors:

Deepak Krishnamurthy, Francois benoit du Rey and Ethan Li