ykjawale / dicot_cmd

Command line DIC Object Tracking (DICOT) code written in MATLAB to analyze DIC image time-series.

DICOT_cmd

Command line DIC Object Tracking (DICOT) code written in MATLAB to analyze DIC image time-series.
Authors: @athale , @anushreec , @ykjawale , @dhruv

DICOT GUI, with a GUI also available

Reference

Quantifying Intracellular Particle Flows by DIC Object Tracking (DICOT)
A. R. Chaphalkar, Y. K. Jawale, D. Khatri, and C. A. Athale
DOI: ...

Instructions for use:

1. Download the entire folder
2. Open the MATLAB terminal (MATLAB 2017b and higher). To run this code you will need the Image Processing Toolbox to be installed.
3. Change directory to where you downloaded and unzipped the files. At the command line type,

>> DICOT_main_all

4. You will be prompted to open a TIF time-series. Use provided test file, click to select the time-series stored as a multipage TIF test_image.
5. Follow the popup menu to complete the filtering, segmentation and tracking.
6. All output files are stored in a sub-folder ./DICOT_test_image/.
7. Following output files will be generated,
   • trackingmovie.TIF contains the tracked segments for visual inspection
   • segmentedmovie.TIF The time series with the overlaid centers of objects detected (either using RegionMax or centroid),
   • trajectories.txt It contains the trajectory information as,
     ObjID, Frame, X, Y, Length (pixels), Time (frames)
     The time is in frame number unit, and the XY positions in pixel unit, length corresponds to the long-axis length of the object.
   • untracked.txt All object coordinates in x and y-coordinates with frame numbers.