/DICOT

Primary LanguageMATLABGNU General Public License v3.0GPL-3.0

DICOT, a MATLAB-based software developed for 2D particle tracking in DIC images
Authors: Anushree Chaphalkar, Yash Jawale, Dhruv Khatri, Chaitanya Athale

License: GPL v3 GitHub release

🔬 💻

DICOT cmd command-line version 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: 10.1016/j.bpj.2020.12.013

Links

Versions and requirements

Version 1.0.0

  • MATLAB R2019b or higher
  • Toolboxes – Image Processing, Statistics, Curve Fitting

Installation

  • As a MATLAB App
    Download and run the DICOT.mlappinstall file on your machine. The DICOT app gets installed in the ‘Apps’ section of your MATLAB environment.
  • from source code 📦
    Download the entire DICOT folder from GitHub and add it to your MATLAB path. Following command will open the DICOT interface. 
    run dicot.mlapp
    Alternatively, you may open the interface directly by double clicking the dicot.mlapp file in the downloaded folder.

User Guide

DICOT GUI looks like as following,

NOTE: Please resize or scroll the app in case it does not display optimally on your screen.

Workflow

  • Opening Image

    • DICOT supports TIFF format
    • Open 📂 image files using,
    File > Open Image Series

  • Image Parameters

    • Frames frames to be analysed
    • Units unit of physical distance
    • Pixel size pixel-to-distance scaling factor
    • Time interval time interval between two consecutive image-frames

  • Object Detection
    Parameters

    • Filter type segmentation filter choice
    • Object type White or Black on background
    • Kernel size size of kernel (typically ≥ object size)
    • Sigma standard deviation of filter
    • Sensitivity tunes detection (for SoG)

    Detection can be done using,

    Operations > Detect Objects

  • Tracking
    Parameters

    • Search radius a threshold distance for linking centroids (approximate distance moved by objects in between two frames)
    • Minimum track time only tracks spanning greater than threshold are retained

    Tracking can be done using,

    Operations > Track Objects

  • Quantification 📈
    Statistics 📊 can be obtained using,

    Operations > Statistics

  • Saving data 💾
    Images 📃 can be saved using,

    File > Save Image

    Movie 🎦 can be saved using,

    Operations > Make movie

    Parameters 📝 can be saved using,

    File > Save Parameters as > TYPE

  • Reset ↪️ parameters
    Reset to default using button

  • Help ❔
    Access Help using button