Embedded Files
PyPOLAR
PyPOLAR
Version 2.8.0 (March 7, 2025)
PyPOLAR 2.8.0 provides more flexibility by allowing the import of ROIs from the ROI Manager of ImageJ/Fiji. The ROI Manager in PyPOLAR further displays ILow values that can now be changed. Bugs with respect to the saving of csv/excel files in the Edge detection mode and to the renumbering of ROIs in the ROI manager were corrected.
Version 2.7.0 (January 6, 2025)
PyPOLAR 2.7.0 includes additional save output formats for more flexibility with data post-processing, notably the possibility to export the measured parameters per pixel in a .csv format as well as composite image files compatible with ImageJ/Fiji. For SHG, in addition to the parameter S, the parameters S2 and S4 are also included.
Version 2.6.4 (October 21, 2024)
PyPOLAR 2.6.4 improves the registration for 4 POLAR with a more ergonomic display of the registration. Minor bugs have been corrected regarding the slicing upon registration. Some error messages are now displayed when the wrong calibration is selected. PyPOLAR 2.6.4 includes now a link to create and customize the colorbars used in the analysis. Additional bugs were corrected concerning, e.g., the computation of the dark value. The pickle option for saving results has been removed.
Version 2.6.2 (December 22, 2023)
PyPOLAR 2.6.2 improves the registration for 4POLAR. A possibility to change the SIFT parameters (contrastThreshold, sigma) is introduced. Tuning these parameters allows for a better registration. The values of these parameters are exported in the Excel file.
The registration is now decoupled from the choice of order for the polarization angles in 4POLAR techniques.
Version 2.6.1 (October 19, 2023)
PyPOLAR 2.6.1 improves the rescaling of the window/app. It includes the possibility to create an ROI from the Crop Manager once coordinates of the zoom are entered. There is now the possibility to save figures and reopen them for later use (.pyfig extension to be selected in the Options tab, Save output). The 4POLAR 2D technique has been now implemented. In addition, it corrects a series of minor bugs (notably, in the edge detection tool).
Version 2.5 (May 25, 2023)
PyPOLAR 2.5 corrects a series of minor bugs. It improves the ROI Manager (with interactive modifications); it includes the possibility to measure orientations with respect to a reference angle.
Version 2.4.4 (March 20, 2023)
PyPOLAR 2.4.4 corrects a series of minor bugs. This version features a button for histogram concatenation. It includes the possibility of choosing the number of bins for histograms, selecting the formats (.pdf, .jpeg, .png, .tif) for saving figures, and entering the pixel size to measure distances in μm.
Version 2.4.3 (March 13, 2023)
PyPOLAR 2.4.3 corrects a number of bugs from 2.4. Colorblind-friendly colormaps are now implemented. The navigation toolbar embedded with the Tkinter canvas has been redesigned for clarity. Additional post-processing options have been included (add axes on all figures, change colormaps, add or remove colorbars, redraw histograms per ROI).
Version 2.4 (February 2, 2023)
PyPOLAR 2.4 features an edge detection module to compute the edges of the intensity image, and compute orientation angles with respect to these edges (contours).
As of February 2, 2023, the MATLAB-based app Polarimetry Contour will no longer be maintained
Version 2.3 (January 28, 2023)
PyPOLAR 2.3 features an ROI manager which allows the user to work flexibly and interactively with multiple ROIs. The user can assign to each ROI a name and a group, select/deselect ROIs to analyze, or delete specific or all ROIs. The list of ROIs can further be saved and reloaded at the user's convenience for later analysis.
Version 2.2 (January 22, 2023) Polarimetry Analysis goes pythonic!
PyPOLAR 2.2 uses Python code to extend the polarimetry analysis to include one-photon fluorescence (1PF), CARS, SRS, SHG, two-photon fluorescence (2PF) and 4POLAR 3D fluorescence. Provides the possibility to change the experimental offset angle as well as to choose the sense of polarization used for the calibration. Includes new features: monitoring the intensity per pixel in the image, saving the polar stack as an animated GIF, measuring distances in image, saving in the excel file additional parameters used for the analysis (dark value, offset, polarization, binning), drawing freehand ROIs, possibility to crop figures, modify the density of sticks and adding axes to the figures post-processing. Increased flexibility by saving the analysis as a compressed pickle file (.pbz2): reloading this file allows the user to re-generate the graphs of interest. Images shown within the application (Intensity and Thresholding tabs) can now be saved in a variety of formats. "4POLAR 2D" and "Edge detection" are under construction.
As of January 23, 2023, the MATLAB-based app Polarimetry will no longer be maintained
Polarimetry
Polarimetry
Version 2.0 (May 10, 2022)
extends the polarimetry analysis beyond one-photon fluorescence (1PF) to include CARS, SRS, SHG and two-photon fluorescence (2PF). Includes new features (displaying and saving a polar stack, erasing ROIs, saving figures in png format, option to differentially change stick density in horizontal vs vertical pixels, possibility to change the experimental offset angle, possibility to change the min and max values for the color-coding of variables). Fixes minor bugs related to binning.
Careful! For 1PF analysis, the Offset Angle must be changed from "100" to "80" to account for rho angles now shown with a counter-clockwise orientation. This bug will be fixed in future versions.
Version 1.4.4 (August 14, 2020)
fixes bug related to the use of batch processing, includes link to present website for checking updates and an "end of analysis" alert message for batch analysis, and provides a choice of distortion-corrected disc cones to use for analysis depending on the wavelength and acquisition date
Version 1.3.6 (June 18, 2020)
Introduces the possibility to export the combined ROI/intensity thresholded image as a mask for further analysis. Fixes a bug related to the use of the "figure rotation" feature.
Version 1.3.3 (April 15, 2020)
fixes bugs related to the use of multiple ROIs, and introduces the possibility to export the used ROIs, or intensity thresholded image, as a mask for further analysis (for example, multi-color polarimetry/imaging)
Data post-processing with Python
Data post-processing with Python
The polarimetry data are saved in a .mat (MATLAB®) file. Post-processing can be naturally done in MATLAB®. For open-source purposes, the .mat data file can be read in Python using the scipy.io library and data plotted using libraries like matplotlib, plotly, seaborn... Here is an example for plotting histograms:
from scipy.io import loadmat
import matplotlib.pyplot as plt
import seaborn as sns
data = loadmat('B16_P36.mat')
Psi = data['Psi']
Rho = data['Rho']
f, ax = plt.subplots(1,1)
ax.set_xlabel('Angle')
ax.set_ylabel('Frequency')
sns.distplot(Psi, bins=20, label='Psi Histogram', color='purple')
sns.distplot(Rho, bins=60, label='Rho Histogram', color='blue')
ax.legend(loc='upper right')
ax.set_xlim([0, 180])
plt.show()
Data post-processing with Matlab
Data post-processing with Matlab
Shifted histograms /Polarimetry/AdditionalFiles/ShiftedHisto.m
Concatenated shifted histograms /Polarimetry/AdditionalFiles/ConcatShiftedHisto.m
Rescaled and concatenated shifted histograms /Polarimetry/AdditionalFiles/RescaledConcatShiftedHisto.m
Horizontal boxplots of psi values /Polarimetry/AdditionalFiles/BoxplotPsiHorizontal.m
Rescales figures of psi values /Polarimetry/AdditionalFiles/RescaledPsiFigs.m
Zoom over an ROI of defined size /Polarimetry/AdditionalFiles/ZoomROI.mlx
Colorbars used in PyPOLAR
Colorbars used in PyPOLAR
PyPOLAR uses a set of colorbars for each output variable. These colorbars can be vizualized and customized using:
the Python script: /Polarimetry/AdditionalFiles/colorbars.py
the Jupyter Notebook on Google Colab
Contacts
Contacts
Cristel Chandre (CNRS)
Manos Mavrakis (CNRS)
Sophie Brasselet (CNRS)
Copyright (c) 2019 Cristel Chandre.
All rights reserved.
Redistribution and use in source and binary forms are permitted provided that the above copyright notice and this paragraph are duplicated in all such forms and that any documentation, advertising materials, and other materials related to such distribution and use acknowledge that the software was developed by the CNRS. The name of the CNRS may not be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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