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
Quantifying Intracellular Particle Flows by DIC Object Tracking (DICOT)
A. R. Chaphalkar, Y. K. Jawale, D. Khatri, and C. A. Athale
DOI: 10.1016/j.bpj.2020.12.013
- Download the entire folder
- Open the MATLAB terminal (MATLAB 2017b and higher). To run this code you will need the Image Processing Toolbox to be installed.
- Change directory to where you downloaded and unzipped the files. At the command line type,
>> DICOT_main_all
- 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.
- Follow the popup menu to complete the
filtering
,segmentation
andtracking
. - All output files are stored in a sub-folder ./DICOT_test_image/.
- 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)
Thetime
is in frame number unit, and theXY
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.