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

🔬 💻

DICOT cmd command-line version also available

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

Links

• Source code
• CyCelS Software

Version 1.0.0

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

• 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.

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