pyMINFLUX

A cross-platform tool for MINFLUX data visualization and filtering.

pyMINFLUX 0.5.0 released!

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We are happy to announce the immediate availability of pyMINFLUX 0.5.0: https://github.com/bsse-scf/pyMINFLUX/releases/tag/0.5.0

Notable additions to pyMINFLUX 0.5.0 are:

  • high-performance 3D viewer for localization plotting
  • colorbar for 2D and 3D plots when color-coding by depth and time
  • new pyminflux.reader.MSRReader for data and metadata from associated MSR file
  • support for importing confocal images from MSR files to display along with the MINFLUX localizations.

Have fun with pyMINFLUX!

pyMINFLUX 0.4.1 released!

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This version fixes a few bugs, significantly speeds up several operations, and adds a few new features; notably it adds an option to pool DCR values for all relocalized iterations (weighted by their photon count) to make the color unmixing significantly more robust.

New features

  • Add Importer option to pool DCR values for all relocalized iterations weighted by their photon count.
  • More efficient calculation of tracking-related statistics.
  • Allow exporting all Analyzer plots in one action (issue/13).
  • When exporting plots, default to input dataset folder in the Save dialog (issue/12).
  • Allow measuring distances in the main Plotter along all spatial directions.
  • Implement automatic update check (currently fixed at 1-week interval).
  • Switch to new build mode (Nuitka) for faster application startup and execution.

Bug fixes

  • Fix pyminflux_reader.py plug-in incompatibility with ParaView 5.12 (issue/14).
  • Fix issue with fluorophore colors being reassigned at random after unmixing.
  • Only calculate and export tracking statistics for tracking datasets.
  • Do not allow plotting average localization of tracking datasets.
  • Fix issue with application packaging that caused some *.npy files to fail reading (issue/11).

You can download the latest version of pyMINFLUX (0.4.1) from https://github.com/bsse-scf/pyMINFLUX/releases/latest.

All other links to documentation, API, issue trackers can be found on the official project page on https://pyminflux.ethz.ch.

pyMINFLUX 0.4.0 released!

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This new release adds compatibility with custom MINFLUX sequences and single-molecule tracking datasets. 

Download: https://github.com/bsse-scf/pyMINFLUX/releases

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.

pyMINFLUX 0.3.0 released!

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Highlights of pyMINFLUX 0.3.0 are the new native file format (that preserves data and settings), new analysis tools, performance and user-experience improvements, and a ParaView reader plug-in!

Get it here!

Changelog

  • 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.
  • Remove 3D Plotter (in favor of using ParaView and the ParaView reader plug-in).

pyMINFLUX 0.2.0 released!

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The main highlights of pyMINFLUX 0.2.0 are the new FRC Analyzer, a tool that implements Fourier Ring Correlation analysis to track the change of signal resolution over time (thus helping decide when the acquisition can be stopped), and full programmatic access to the pyMINFLUX core library, to make it possible to develop analysis pipelines (i.e., Python scripts or Jupyter Notebooks) that run without the user interface. More information is listed in the changelog below.

Changelog

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.
  • Add menu action to check for application updates.

Bug fixes

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

pyMINFLUX 0.1.3 released!

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We are happy to announce the release and immediate availability of pyMINFLUX 0.1.3! This release adds a series of new (and requested) features and fixes a couple of bugs.

New features

  • Implement z-scaling factor to compensate for refractive index mismatch.
  • Add context menu actions to export any plot as a .png image and at a user-defined DPI.
  • 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.

Bug 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.