PhasorPy 0.1 (2024-09-30)

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 phasorpy/phasorpy#1

• Mention FLIMLib by @cgohlke in phasorpy/phasorpy#2

• Mention PhasorIdentifier by @cgohlke in phasorpy/phasorpy#3

• Mention PAM by @cgohlke in phasorpy/phasorpy#4

• Add color module by @cgohlke in phasorpy/phasorpy#5

• Add io and datasets modules by @cgohlke in phasorpy/phasorpy#7

• Add datasets and enable mass downloads by @cgohlke in phasorpy/phasorpy#8

• Add link to GitHub repo by @cgohlke in phasorpy/phasorpy#9

• Update .gitignore by @cgohlke in phasorpy/phasorpy#14

• Add link to FLIM LABS GitHub by @cgohlke in phasorpy/phasorpy#16

• Improve contributing guide and create PR template by @cgohlke in phasorpy/phasorpy#15

• Update workflows by @cgohlke in phasorpy/phasorpy#18

• Enable Dependabot version updates for actions by @cgohlke in phasorpy/phasorpy#22

• Bump the github-actions group with 3 updates by @dependabot in phasorpy/phasorpy#23

• Update copyright year by @cgohlke in phasorpy/phasorpy#24

• Add read functions for PTU, FBD, and FLIF files by @cgohlke in phasorpy/phasorpy#25

• Fix target-version for black 24.1 by @cgohlke in phasorpy/phasorpy#29

• Mention tttrlib by @cgohlke in phasorpy/phasorpy#30

• Add calibration functions to the phasor module by @bruno-pannunzio in phasorpy/phasorpy#28

• Various additions and improvements to the phasor module by @cgohlke in phasorpy/phasorpy#32

• Fix datasets.fetch with pooch 1.8.1 by @cgohlke in phasorpy/phasorpy#34

• Add phasor_from_signal function by @cgohlke in phasorpy/phasorpy#35

• Mention code contributions by @cgohlke in phasorpy/phasorpy#38

• Add plot module by @cgohlke in phasorpy/phasorpy#36

• Fix PhasorPlot.semicircle changes axes limits by @cgohlke in phasorpy/phasorpy#39

• Fix contour offsets by @cgohlke in phasorpy/phasorpy#40

• Higher level calibration function by @bruno-pannunzio in phasorpy/phasorpy#37

• Hide typehints in API documentation by @cgohlke in phasorpy/phasorpy#41

• Add skip_axes parameter to phasor_calibrate function by @bruno-pannunzio in phasorpy/phasorpy#42

• Additions and improvements to the phasor module by @cgohlke in phasorpy/phasorpy#44

• Improve typing by @cgohlke in phasorpy/phasorpy#45

• Add dtime parameter to read_ptu function by @cgohlke in phasorpy/phasorpy#46

• Add phasor_from_fret functions by @cgohlke in phasorpy/phasorpy#49

• Bump the github-actions group with 1 update by @dependabot in phasorpy/phasorpy#50

• Use Scientific Python SPEC0 instead of NEP29 by @cgohlke in phasorpy/phasorpy#51

• Add interactive FRET phasor plot by @cgohlke in phasorpy/phasorpy#52

• Add PhasorPlot.cursor method by @cgohlke in phasorpy/phasorpy#53

• Fix linting errors in Cython code by @cgohlke in phasorpy/phasorpy#54

• Improve phasor_from_lifetime tutorial by @cgohlke in phasorpy/phasorpy#55

• Add functions to convert optimal frequency and lifetime by @cgohlke in phasorpy/phasorpy#56

• Mention napari-live-flim by @cgohlke in phasorpy/phasorpy#57

• Mention HySP software by @cgohlke in phasorpy/phasorpy#58

• Add functions to convert between lifetime fractions and amplitudes by @cgohlke in phasorpy/phasorpy#60

• Add components module by @bruno-pannunzio in phasorpy/phasorpy#59

• Support NumPy 2 by @cgohlke in phasorpy/phasorpy#61

• Build with NumPy 2 by @cgohlke in phasorpy/phasorpy#62

• Bump peaceiris/actions-gh-pages from 3 to 4 in the github-actions group by @dependabot in phasorpy/phasorpy#64

• Format docstring examples with blackdoc by @cgohlke in phasorpy/phasorpy#66

• Add phasor_at_harmonic function by @cgohlke in phasorpy/phasorpy#65

• Fix phasor_calibrate function to handle multi harmonic calibration by @bruno-pannunzio in phasorpy/phasorpy#69

• Mention FLIMfit software by @cgohlke in phasorpy/phasorpy#70

• Fix spelling by @cgohlke in phasorpy/phasorpy#72

• Bump pypa/cibuildwheel from 2.17.0 to 2.18.1 in the github-actions group by @dependabot in phasorpy/phasorpy#71

• Numpy 2 is released by @cgohlke in phasorpy/phasorpy#73

• Mention HORIBA EzTime software by @cgohlke in phasorpy/phasorpy#75

• Use phasorpy-data repo instead of Zenodo in GitHub Actions by @cgohlke in phasorpy/phasorpy#74

• Enable code coverage via codecov.io by @cgohlke in phasorpy/phasorpy#76

• Bump pypa/cibuildwheel from 2.18.1 to 2.19.1 in the github-actions group by @dependabot in phasorpy/phasorpy#77

• Seed random number generator with constant in tutorials by @cgohlke in phasorpy/phasorpy#80

• Add graphical component analysis in components module by @bruno-pannunzio in phasorpy/phasorpy#79

• Add cursors module by @schutyb in phasorpy/phasorpy#48

• Add geometric helper functions by @cgohlke in phasorpy/phasorpy#81

• Improve cursors module by @cgohlke in phasorpy/phasorpy#82

• Add function to project multi-harmonic phasor coordinates onto principal plane by @cgohlke in phasorpy/phasorpy#78

• Add elliptic cursors by @cgohlke in phasorpy/phasorpy#84

• Add phasor_to_signal function by @cgohlke in phasorpy/phasorpy#86

• Add median filtering function by @bruno-pannunzio in phasorpy/phasorpy#85

• Bump pypa/cibuildwheel from 2.19.1 to 2.19.2 in the github-actions group by @dependabot in phasorpy/phasorpy#89

• Sort fractions in PhasorPlot.components by @cgohlke in phasorpy/phasorpy#90

• Fix type of harmonic parameter in phasor_to_signal by @cgohlke in phasorpy/phasorpy#91

• Add LFD workshop FLIM tutorial by @cgohlke in phasorpy/phasorpy#63

• Add lifetime_to_signal function by @cgohlke in phasorpy/phasorpy#93

• Use Cython>=3.0.11 by @cgohlke in phasorpy/phasorpy#94

• Fix phasor_center with NaN input by @cgohlke in phasorpy/phasorpy#96

• Fix RuntimeWarning in plot_phasor_image by @cgohlke in phasorpy/phasorpy#97

• Unify phasor_from_signal functions by @cgohlke in phasorpy/phasorpy#98

• Add phasor_threshold function to phasor module by @bruno-pannunzio in phasorpy/phasorpy#88

• Fix undefined and not defined function names in _utils module by @bruno-pannunzio in phasorpy/phasorpy#100

• Improve handling of NaN values by @cgohlke in phasorpy/phasorpy#101

• Add default fractions to graphical_component_analysis by @bruno-pannunzio in phasorpy/phasorpy#103

• Improve tutorials by @cgohlke in phasorpy/phasorpy#102

• Support writing multi-harmonic phasors to OME-TIFF by @cgohlke in phasorpy/phasorpy#104

• Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 in the github-actions group by @dependabot in phasorpy/phasorpy#107

• Do not test wheels on Python 3.13 for now by @cgohlke in phasorpy/phasorpy#108

• Add dataset from zenodo.org/records/13625087 by @cgohlke in phasorpy/phasorpy#109

• Test minimum runtime requirements by @cgohlke in phasorpy/phasorpy#110

• Add EOSS badge and use recommended language by @cgohlke in phasorpy/phasorpy#111

• Improve io module by @cgohlke in phasorpy/phasorpy#112

• Disable scikit-learn in requirements_min.txt for now by @cgohlke in phasorpy/phasorpy#113

• Configure pre-commit hooks by @cgohlke in phasorpy/phasorpy#114

• Enable mypy strict mode by @cgohlke in phasorpy/phasorpy#115

• Configure mypy enable_error_code by @cgohlke in phasorpy/phasorpy#116

• Configure mypy for tests and tutorials by @cgohlke in phasorpy/phasorpy#117

• Revise phasor_from_ometiff by @cgohlke in phasorpy/phasorpy#119

• Increase API documentation toctree depth by @cgohlke in phasorpy/phasorpy#120

• Mention FLIMPA software by @cgohlke in phasorpy/phasorpy#121

• Publish docs in subfolder by @cgohlke in phasorpy/phasorpy#123

• Use Sphinx dirhtml by @cgohlke in phasorpy/phasorpy#125

• Add links to PyPI and Zenodo to readme by @cgohlke in phasorpy/phasorpy#126

• Update project URLs by @cgohlke in phasorpy/phasorpy#127

• Update pull request template by @cgohlke in phasorpy/phasorpy#128

• Change release-pypi to build_sdist workflow by @cgohlke in phasorpy/phasorpy#129

• Enable testing wheels on Python 3.13 by @cgohlke in phasorpy/phasorpy#131

• Release v0.1 by @cgohlke in phasorpy/phasorpy#130

New Contributors

• @cgohlke made their first contribution in phasorpy/phasorpy#1

• @dependabot made their first contribution in phasorpy/phasorpy#23

• @bruno-pannunzio made their first contribution in phasorpy/phasorpy#28

• @schutyb made their first contribution in phasorpy/phasorpy#48

Full Changelog: phasorpy/phasorpy