hsipy 1.0.5

Python Module to do Hypespectral Imaging Analysis using the Phasor Transform

hsipy: Is a Python module to perform phasor analysis and visualization.

Hyperspectral imaging (HSI) have become paramount in biomedical science. The power of the combination between traditional imaging and spectroscopy opens the possibility to address information inaccessible before. For bioimaging analysis of these data, the Phasor Plots are tools that help the field because of their straightforward approach. Thus it is becoming a key player in democratizing access to HSI, and improve open source software for bioimaging communities.

hsipy is a module for HSI data analysis using the phasor approach. The phasor approach was developed as model free method and relies on the Fourier Transform properties.

Documentation

[Git Repository] https://github.com/schutyb/rep-hsipy

Phasor Analysis

Considering an hyperspectral image stack, the fluorescence spectra at each pixel can be transformed in phasor coordinates (G (λ)) and (S (λ)) as described in the following equations. I(λ) represent the intensity at every wavelength (channel), n is the number of the harmonic and λ i the initial wavelength. The, x and y coordinates are plotted in the spectral phasor plot.

$$ G(\lambda) = \frac{\int_L I(\lambda) cos\left( 2\pi n \frac{\lambda - \lambda_i}{\lambda_{max} - \lambda_{min}} \right)}{\int_L I(\lambda)d\lambda}$$

$$ S(\lambda) = \frac{\int_L I(\lambda) sen\left( 2\pi n \frac{\lambda - \lambda_i}{\lambda_{max} - \lambda_{min}} \right)}{\int_L I(\lambda)d\lambda} j $$

The angular position in the spectral phasor plot relates to the center of mass of the emission spectrum and the modulus depends on the spectrum’s full width at the half maximum (FWHM). For instance, if the spectrum is broad its location should be close to the center. Otherwise, if there is a red shift in the spectrum, its location will move counterclockwise toward increasing angle from position (1, 0). Spectral phasors have the same vector properties as lifetime phasors. A detailed description of the spectral phasor plot properties can be found in Malacrida et al. 1.

Installation

  pip install hsipy
  conda install hsipy

Authors

• @schutyb

License

bsd-3-clause

Contributing

Contributions are always very well welcome. The PhasorPy library intends to create an open-source and collaborative community between spectroscopy and fluorescence microscopy users with the same functionalities as SimFCS but accessible and self-sustainable in the long term as other Python libraries and communities.

References

[1] Malacrida, L., Gratton, E. & Jameson, D. M. Model-free methods to study membrane environmental probes: A comparison of the spectral phasor and generalized polarization approaches. Methods Appl. Fluoresc. 3, 047001 (2015).