Resources

Matlab Apps

• Fit Landau Fan Diagram for 2DEG: Fits transport data (Rxx vs V_BG vs H) of 2DEG to Landau Fan diagram for different values of cpacitance.
  Steps to follow:
  1. Save your transport data as .mat file, where the resistance or voltage data is saved as a struct named 'transport_data', where each field contains double array of Rxx or Rxy etc. The same .mat file should contain magnetic field data as a vector named 'H' and gate voltage data as a vector named 'Vbg'
  2. Load the transport data, press 'Load Data/Plot'
  3. Change 'Field factor' to 1, if the applied magnetic field is exactly known
  4. Change 'Capacitance' value in units of 1/(V.cm^2)
  5. Fix 'Number of LL'
  6. Choose value of origin for the Landau fan in units of Vbg (for example Charge Neutrality or other filling fractions)
  7. Choose 'Degeneracy' in integer
  8. Press 'Fit'
  9. You can change Axis limits, colorbar limits and can choose which Colormap to use
  10. Once fitted, you can export values of capacitance (c_cm), field factor (field_factor) and value of origin of Landau fan (V0) to workspace for future use
  11. 'Export to workspace' also saves the fitted figure as PNG in the directory where the .mat file is saved

• Calculate Innervation Index of the Sensory Neuron Terminals (developed with Swagata Dey): This app loads tiff images of neuron terminals in footpad saved in a single folder. It then lets the user crop the image by either freehand drawing or polygon. The user can choose a thresholding method, either binary thresholding or Otsu's method and calculates the Innervation index and saves it as a txt file in the same folder. The user can access the intermediate steps from .MAT file saved in same folder.
  Steps to follow:
  1. Put all your tif or tiff images in a folder
  2. Run the .mlapp file
  3. In the app window, press on "Load Folder" and browse to select the desired folder
  4. Then set the "Cut off Algorithm" to either "1-0 Cut off" or "Otsu"
  5. For "1-0 Cut off", enter "Cut off Value" (Cut off value is not normalized. It is shade of gray out of 2^16 = 65536 shades. For example 2500 is 0.0385 on a 0-1 scale of gray.)
  6. Choose "Crop Options" between "Polygon" and "Freehand"
  7. Press "Calculate"
  8. Crop the desired region of interest (ROI) and the app asks whether another fine cropping is needed just for the purpose of noise reduction
  9. The innervation index is calculated and is saved in the same folder as a TXT file, where the first column is name of the Image file and the second column is innervation index value
  10. All the calculation steps are saved as a MATLAB Workspace (.mat) file in the same folder
  (Technically this app can load any tiff or tif image in grayscale and can calculate the ratio of the number of white pixels and the total number of pixels within a user specified region of interest by either Otsu's method to find a threshold of white/black or a threshold defined by the user.)