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
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.
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.
To change track parameters such as Pixel size, chamber dimensions etc., navigate to Edit > Track parameters or hit 'Ctrl + T'.
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.
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'.
- 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
@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}
}
Deepak Krishnamurthy, Francois benoit du Rey and Ethan Li