PhasorPy is an open-source Python library for the analysis of fluorescence lifetime and hyperspectral images using the phasor approach.

This is the third alpha release of the PhasorPy library. It fixes the averaging of phasor coordinates in the phasor_center and phasor_calibrate functions, replaces the phasor_filter function with phasor_filter_median, adds support for multiple harmonics to phasor_threshold, and adds the read_imspector_tiff function to read ImSpector FLIM TIFF files. This release supports Python 3.10 to 3.13.

What's Changed

• Bump version by @cgohlke in #152
• Bump the github-actions group with 2 updates by @dependabot in #153
• Mention GSLab software by @cgohlke in #156
• Mention BrightEyes software by @cgohlke in #157
• Pin numpy<2.2.0 for static code analysis by @cgohlke in #159
• Fix mypy errors with matplotlib-3.10 by @cgohlke in #160
• Fix averaging phasor coordinates and related issues by @cgohlke in #155
• Add support for ImSpector FLIM TIFF files by @cgohlke in #161
• Release v0.3 by @cgohlke in #162

Full Changelog: v0.2...v0.3

PhasorPy is an open-source Python library for the analysis of fluorescence lifetime and hyperspectral images using the phasor approach.

This is the second alpha release of the PhasorPy library. It fixes NaN handling in the median filter, simplifies multiple harmonic calibration, and adds functions for spectral vector denoising and Anscombe transformation. This release supports Python 3.10 to 3.13.

What's Changed

• Bump version by @cgohlke in #132
• Add documentation version switcher config file by @cgohlke in #134
• Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 in the github-actions group by @dependabot in #133
• Update FLUTE license by @cgohlke in #137
• Support Linux on AArch64 by @cgohlke in #135
• Improve private parse_harmonic function by @cgohlke in #138
• Add Anscombe transformation functions by @cgohlke in #139
• Mention PhasorPlots for dummies by @cgohlke in #140
• Simplify multiple harmonic calibration by @bruno-pannunzio in #124
• Add documentation version switcher dropdown by @cgohlke in #136
• Mention AlliGator software by @cgohlke in #141
• Bump pypa/cibuildwheel from 2.21.1 to 2.21.3 in the github-actions group by @dependabot in #144
• Add tool to print SHA256 hashes of dataset files by @cgohlke in #143
• Add Convallaria dataset by @bruno-pannunzio in #145
• Mention LIFA software by @cgohlke in #146
• Upgrade GitHub Actions to macOS-13 environment by @cgohlke in #149
• Add spectral vector denoising by @cgohlke in #148
• Replace median filter implementation for NaN handling consistency by @bruno-pannunzio in #147
• Improve median filter by @cgohlke in #150
• Release v0.2 by @cgohlke in #151

Full Changelog: v0.1...v0.2

PhasorPy is an open-source Python library for the analysis of fluorescence lifetime and hyperspectral images using the phasor approach.

This is the first alpha release of the PhasorPy library. It contains over 70 documented and tested functions and class methods to calculate, calibrate, filter, transform, store, analyze, and visualize phasor coordinates, as well as to read fluorescence lifetime and hyperspectral signals from PTU, SDT, LSM, and other file formats. Ten tutorials demonstrate the use of the programming interface. An interactive app calculates and plots phasor coordinates of FRET donor and acceptor channels as a function of many model parameters. This release supports Python 3.10 to 3.13.

What's Changed

• Create initial project infrastructure by @cgohlke in #1
• Mention FLIMLib by @cgohlke in #2
• Mention PhasorIdentifier by @cgohlke in #3
• Mention PAM by @cgohlke in #4
• Add color module by @cgohlke in #5
• Add io and datasets modules by @cgohlke in #7
• Add datasets and enable mass downloads by @cgohlke in #8
• Add link to GitHub repo by @cgohlke in #9
• Update .gitignore by @cgohlke in #14
• Add link to FLIM LABS GitHub by @cgohlke in #16
• Improve contributing guide and create PR template by @cgohlke in #15
• Update workflows by @cgohlke in #18
• Enable Dependabot version updates for actions by @cgohlke in #22
• Bump the github-actions group with 3 updates by @dependabot in #23
• Update copyright year by @cgohlke in #24
• Add read functions for PTU, FBD, and FLIF files by @cgohlke in #25
• Fix target-version for black 24.1 by @cgohlke in #29
• Mention tttrlib by @cgohlke in #30
• Add calibration functions to the phasor module by @bruno-pannunzio in #28
• Various additions and improvements to the phasor module by @cgohlke in #32
• Fix datasets.fetch with pooch 1.8.1 by @cgohlke in #34
• Add phasor_from_signal function by @cgohlke in #35
• Mention code contributions by @cgohlke in #38
• Add plot module by @cgohlke in #36
• Fix PhasorPlot.semicircle changes axes limits by @cgohlke in #39
• Fix contour offsets by @cgohlke in #40
• Higher level calibration function by @bruno-pannunzio in #37
• Hide typehints in API documentation by @cgohlke in #41
• Add skip_axes parameter to phasor_calibrate function by @bruno-pannunzio in #42
• Additions and improvements to the phasor module by @cgohlke in #44
• Improve typing by @cgohlke in #45
• Add dtime parameter to read_ptu function by @cgohlke in #46
• Add phasor_from_fret functions by @cgohlke in #49
• Bump the github-actions group with 1 update by @dependabot in #50
• Use Scientific Python SPEC0 instead of NEP29 by @cgohlke in #51
• Add interactive FRET phasor plot by @cgohlke in #52
• Add PhasorPlot.cursor method by @cgohlke in #53
• Fix linting errors in Cython code by @cgohlke in #54
• Improve phasor_from_lifetime tutorial by @cgohlke in #55
• Add functions to convert optimal frequency and lifetime by @cgohlke in #56
• Mention napari-live-flim by @cgohlke in #57
• Mention HySP software by @cgohlke in #58
• Add functions to convert between lifetime fractions and amplitudes by @cgohlke in #60
• Add components module by @bruno-pannunzio in #59
• Support NumPy 2 by @cgohlke in #61
• Build with NumPy 2 by @cgohlke in #62
• Bump peaceiris/actions-gh-pages from 3 to 4 in the github-actions group by @dependabot in #64
• Format docstring examples with blackdoc by @cgohlke in #66
• Add phasor_at_harmonic function by @cgohlke in #65
• Fix phasor_calibrate function to handle multi harmonic calibration by @bruno-pannunzio in #69
• Mention FLIMfit software by @cgohlke in #70
• Fix spelling by @cgohlke in #72
• Bump pypa/cibuildwheel from 2.17.0 to 2.18.1 in the github-actions group by @dependabot in #71
• Numpy 2 is released by @cgohlke in #73
• Mention HORIBA EzTime software by @cgohlke in #75
• Use phasorpy-data repo instead of Zenodo in GitHub Actions by @cgohlke in #74
• Enable code coverage via codecov.io by @cgohlke in #76
• Bump pypa/cibuildwheel from 2.18.1 to 2.19.1 in the github-actions group by @dependabot in #77
• Seed random number generator with constant in tutorials by @cgohlke in #80
• Add graphical component analysis in components module by @bruno-pannunzio in #79
• Add cursors module by @schutyb in #48
• Add geometric helper functions by @cgohlke in #81
• Improve cursors module by @cgohlke in #82
• Add function to project multi-harmonic phasor coordinates onto principal plane by @cgohlke in #78
• Add elliptic cursors by @cgohlke in #84
• Add phasor_to_signal function by @cgohlke in #86
• Add median filtering function by @bruno-pannunzio in #85
• Bump pypa/cibuildwheel from 2.19.1 to 2.19.2 in the github-actions group by @dependabot in #89
• Sort fractions in PhasorPlot.components by @cgohlke in #90
• Fix type of harmonic parameter in phasor_to_signal by @cgohlke in #91
• Add LFD workshop FLIM tutorial by @cgohlke in #63
• Add lifetime_to_signal function by @cgohlke in #93
• Use Cython>=3.0.11 by @cgohlke in #94
• Fix phasor_center with NaN input by @cgohlke in #96
• Fix RuntimeWarning in plot_phasor_image by @cgohlke in #97
• Unify phasor_from_signal functions by @cgohlke in #98
• Add phasor_threshold function to phasor module by @bruno-pannunzio in #88
• Fix undefined and not defined function names in _utils module by @bruno-pannunzio in #100
• Improve handling of NaN values by @cgohlke in #101
• Add default fractions to graphical_component_analysis by @bruno-pannunzio in #103
• Improve tutorials by @cgohlke in #102
• Support writing multi-harmonic phasors to OME-TIFF by @cgohlke in #104
• Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 in the github-actions group by @dependabot in #107
• Do not test wheels on Python 3.13 for now by @cgohlke in #108
• Add dataset from zenodo.org/records/13625087 by @cgohlke in #109
• Test minimum runtime requirements by @cgohlke in #110
• Add EOSS badge and use recommended language by @cgohlke in #111
• Improve io module by @cgohlke in #112
• Disable scikit-learn in requirements_min.txt for now by @cgohlke in #113
• Configure pre-commit hooks by @cgohlke in #114
• Enable mypy strict mode by @cgohlke in #115
• Configure mypy enable_error_code by @cgohlke in...