0.6.0

Changelog

Main feature of pyMINFLUX 0.6.0 is the native support all input formats from Imspector version m2410.

New features

• Add support for importing data in the formats .npy .mat., .json, and .zarr from Imspector version m2410 and newer.
• Initial support for reading and storing beamline monitoring data from .zarr files.
• Read and add fbg parameter to data viewer and histogram plotter.
• Rename "DCR Unmixing" to "Multiplexing" in Wizard.
• Allow showing average localization for XZ and YZ projections.
• Warn before importing non-relocalized iterations if the minimum number of localizations per trace is larger than one.

Bug fixes

• Make estimation of which iterations relocalize more robust.
• Make scanning of detectors in MSR files more robust.

Troubleshooting

Since the pyMINFLUX.exe and pyMINFLUX.app applications are not (yet) digitally signed, both Windows and macOS may prevent the application from starting. If you encounter any problem, please have a look at our troubleshooting guide.

0.5.0

Changelog

This version fixes a few bugs and adds a few new features; notably it adds a built-in 3D viewer, new color-coding options and the possibility of adding a confocal image as canvas background directly from an MSR file.

New features

• Add high-performance 3D viewer for localization plotting.
• Allow loading confocal images from MSR files to display along with the MINFLUX localizations.
• Add pyminflux.reader.MSRReader class to API to load both data and metadata from MSR files.
• Expand list of options (nothing, tid, fluorophore, depth, time) for color-coding.
• All parameters can now be color-coded.
• Add colorbar to the 2D and 3D plots when color-coding by depth and time.
• Allow color unmixing on filtered dataset.
• Always calculate the total trace duration, not only for tracking datasets.
• Add "Export all plots" option to the context menu of the results histograms in the Analyzer.
• Add parameter "tim_tot" to the list of options in the Histogram Plotter.
• Allow exporting 3D plots and colorbars as high-resolution PNG images.

Bug fixes

• Run global filters after updating the min trace length in the MinFluxProcessor.
• Fix the x-axis limits in the Color Unmixer for the DCR histogram to (0.0, 1.0).

Troubleshooting

Since the pyMINFLUX.exe and pyMINFLUX.app applications are not (yet) digitally signed, both Windows and macOS may prevent the application from starting. If you encounter any problem, please have a look at our troubleshooting guide.

0.4.1

Changelog

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).

0.4.0

Changelog

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.

0.3.0

Changelog

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

0.2.0

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.
  • Example notebook
• Add menu action to check for application updates.

Fixed

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

0.1.3

Changelog

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.

Fixed

• 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.

0.1.2

Changelog

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

0.1.1

This is the first official release of pyMINFLUX.