Pyminflux

New features

Data compatibility
* Add support for custom MINFLUX sequences.
* Add initial support for single-molecule tracking datasets.
* Update the pyMINFLUX Reader ParaView plugin to read .pmx version 2.0 files.
* Add macOS M1 build of the pyMINFLUX application.

Analysis and filtering tools
* Merge Trace Length Viewer tool into the Analyzer.
* Implement filtering by trace length into the Analyzer.
* Add per-trace tracking stats to the Trace Stats Viewer (tracking datasets only).
* Add Histogram Plotter tool.
* Implement `Set range` context-menu action in the Time Inspector.

UI
* Switch to green-magenta color scheme for fluorophore IDs.
* Add a scale bar to the main data viewer (for XYZ localisations).
* Display line connecting subsequent localizations within a trace (tracking datasets only).

Performance improvements
* Dramatically improve the rendering of color-coded localizations.
* Speed up dataframe-based operations by upgrading to Pandas 2.2.x with PyArrow backend

Fixes

* Fix default axis ranges not being applied to the Analyzer plots when loading new data.
* Fix (incorrectly) forcing the aspect ratio of the Data Plotter for XYZ localizations.

New features

* Add native pyMINFLUX file format `.pmx`.
* FRC Analysis now runs in parallel over all CPU cores.
* Add new Trace Statistics Viewer.
* Add new Trace Length Viewer.
* Add fluorophore ID reassignment within traces by majority vote.
* Allow opening files by drag-and-drop onto the Pipeline Toolbar (left panel).
* Add all analysis tools to the main window's Analysis menu.
* Add companion [ParaView reader plug-in](https://github.com/bsse-scf/pyMINFLUX/tree/master/paraview_plugins).
* Remove 3D Plotter (in favor of using ParaView and the ParaView reader plug-in).

New features

* Calculate additional per-trace statistics and allow exporting all stats to csv file.
* Add Fourier Ring Correlation tool to follow resolution progression.
* Allow complete access to the API for command-line/notebook processing: https://pyminflux.ethz.ch/api/pyminflux.
* [Example notebook](examples/processing.ipynb)
* Add menu action to check for application updates.

Fixes

* Fix issue with the fluorophore drop-down menu not being refreshed after global reset button is pressed.

New features

* Implement z-scaling factor to compensate for refractive index mismatch (issue 1).
* Add context menu actions to export any plot as a `.png` image and at a user-defined DPI (issue 3).
* Add global reset button to the main-window wizard and remove the one from the Analyzer.
* Add quick help for all entries in the Options dialog.
* Add links to code repository, issues page, and mailing list to the Help menu.
* Add a few minor UI tweaks.

Fixes

* Fix issue with applying a filter in the Time Inspector not updating the Analyzer plots.
* Fix issue with measurement lines being allowed when the plotted data was not spatial (x, y), and the reported distance would be in nm.
* Fix inconsistency in the way fluorophore IDs and colors were assigned by the various methods used.

Bug fix release.

Fixes

* Fix issue with exporting to `.npy` only working when the `Active Color` selector was on `All`.

First official release.