sarthakjariwala / python_gui_apps

GLabViz - Interactive Analysis and Visualization Application for Scientific Data written in Python using Qt and pyqtrgaph

GLabViz

Graphical User Interface (GUI) Python apps written in python using qt and pyqtgrpah for quick analysis of scientific data. It also includes the ability to convert data to H5 if needed.

Python is not required to use GLabViz (see How to use?)

DOWNLOAD HERE

The primary users for this Python package application are Ginger Lab members at the University of Washington, Seattle but is licensed under MIT License and open for everyone to use.

Includes

• Fluorescence Lifetime Analysis

  • Analyze lifetime
  • Fit data with or without IRF
  • Fit with stretched, single, or double exponential functions by diff_ev or fmin_tnc
  • Calculate surface recombination velocity
  • Export graph and fit results

• Spectra Analysis

  • Analyze single spectrum
    • Fit with or without background and white light
    • Fit with single Lorentzian, single Gaussian, double Gaussian, triple Gaussian models
    • Export graph and fit results
  • Analyze spectra scan
    • Load spectra scan data in .h5 or .pkl files
    • Plot raw scan data
    • Plot scan intensity sums
    • Plot fitted scan by pk_pos, fwhm, sigma, or height
    • Export fitted scan
  • .pkl to .txt, .pkl to .h5 converters

• Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis

  • Load lifetime scans in .h5 or .pkl files
  • Plot histogram intensity sums and analyze PSF
  • Export intensities array and intensities image
  • Plot raw histogram data and analyze lifetime
  • Compare lifetime in two different regions

• Photluminescence Quantum Efficiency (PLQE) Analysis

  • Plot PLQE data
  • Calculate PLQE

• UV-Vis Data Analysis

  • Plot UV-Vis data
  • Correct UV-Vis data for scattering
  • Plot Tauc data
  • Calculate bandgap
  • Export UV-Vis and Tauc plots

• General H5 View and Plot

  • Load .h5 file to view file structure
  • Plot datasets as a graph or an image

• H5 and PKL File Viewer

  • Load .h5 or .pkl file to view file structure

• Image Analysis

  • Load image on SPOT or Pixera settings, or specify pixel size
  • Handle RGB and greyscale images
  • Select magnification
  • Color profile horizontally or vertically

Screenshots

Welcome Screen

Lifetime Analysis

Spectra Analysis

FLIM Analysis

UV-Vis Analysis

H5 & Pkl View

H5 Quick Plot

Image Analysis

How to use?

Standalone App - without Python or any dependencies (only for Windows users, comming soon for Mac users)

• Under the releases page, download the latest release of the DataBrowser zip file
• Extract the zip file and run DataBrowser.exe

With Python and its dependencies

git clone https://github.com/SarthakJariwala/Python_GUI_apps.git

• Install all dependencies
• Run the application by double-clicking DataBrowser.py.
• OR Run it from command-line while in the PythonGUI_apps folder:

python DataBrowser.py

Dependencies

• ScopeFoundry
• pyqtgraph
• numpy
• pyqt
• qtpy
• h5py
• matplotlib
• scipy
• lmfit
• customplotting

Installing dependencies from command-line

conda install numpy pyqt qtpy h5py pyqtgraph
pip install ScopeFoundry
pip install matplotlib scipy lmfit customplotting==0.1.4.dev0

python_gui_apps's Issues

Export Figure - add options to control x axis, yaxis, title, cmap, other plot controls upon selecting Export Figure

Convert spectra scan fit pkl file to h5 file

• Convert lmfit ModelResult file to h5 (only keep the fit data)
• Convert only fit result file (w/o ModelResult) to h5

Include option to smooth traces in Lifetime Analysis

Use numpy.convolve

Fit entire FLIM plot to get lifetime at all pixels

Analyze Point Spread Function needs a better way to correct background

Ideas - user option to select the background or guess better than an array of zeros or fourth-order polynomial fit?

Update Description and Screenshots for release v2.0

• update readme

• Add description text or video or gif for individual analysis tools