by Lynn M. Ostersehlt (1), Daniel C. Jans (1,2), Anna Wittek (1,2), Jan Keller-Findeisen (1), Steffen J. Sahl (1), Stefan W. Hell (1,3,4), and Stefan Jakobs (1,2,4,5)
1 Max Planck Institute for Multidisciplinary Sciences, Department of NanoBiophotonics, Göttingen, Germany 2 University Medical Center Göttingen, Department of Neurology, Göttingen, Germany 3 Max Planck Institute for Medical Research, Department of Optical Nanoscopy, Heidelberg, Germany 4 Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany 5 Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Göttingen, Germany
to appear in Nature Methods
Contact: [email protected]
This is the software package containing raw localization data and analysis scripts in Matlab (https://www.mathworks.com/products/matlab.html). It has been successfully tested with Matlab R2020b.
The source code of the software is licensed under the MIT license (see file LICENSE).
The data is provided for academic and visualization purposes only. Commercial usage of the provided DNA-Paint Minflux nanoscopy data (reproduction outside of the publication, etc. ) is forbidden. Please contact the authors for further inquiries.
No specific installation is necessary. Execute "initialize.m" at least once before running other scripts to include all paths.
Make sure to run initialize.m at least once.
Call "analyse_single_measurements.m" Creates a rendering and a figure containing key data (localization precision, brightness, FRC) for each single measurement used in the main text figures and for all measurements used in the performance analysis in the supplement of the publication.
Call "analyse_measurement_series.m" Creates an Excel file that contains a table of relevant information for all measurement series (laser power, pinhole, ...).
Call "create_supplemental_figures_minflux_performance.m" Recreates Supl. Note figues, performance measures for aggregated measurement series (laser power, pinhole, ...).
Call "create_supplemental_figure_time_series_vimentin.m" Recreates FRC measurements in Supl. Fig. 3, the time series of the Vimentin measurement.
Call "create_supplemental_figures_cfr_simulations.m" Recreates the CFR simulation/estimation from Suppl. Note Figure III.
Files "*.mat" in folder data (subfolder 2D for 2D data and 3D for 3D data). The data files are Matlab "mat" files (based on and compatible with HDF5) and contain the following fields
t - time of each event [s] id - event id (equal value indicates consecutive localization within a single binding event) pos - localization positions X,Y,Z [nm] (for 2D Z = 0) rpos - position of localization relative to beam center in last iteration X,Y,Z [nm] dt - duration of illumination in last iteration [s] efo - average frequency of counts in periphery of illumination pattern [Hz] efc - average frequency of counts in center of illumination pattern [Hz] fbg - est. frequency of counts of the background [Hz]
for each of the localization (so Nx1 or Nx3 vectors)
They are based on the exported output of Abberior Instruments (https://abberior-instruments.com/) exports of measurements on the Abberior Instruments Minflux microscope (https://abberior-instruments.com/products/minflux/). However, the z-coordinate of the localization is already corrected by the factor 0.7 to obtain correct coordinates compared to the output of the Imspector software output. All other field names are identical (except for t, which correnponds to "tim" and lengths have been converted to nm from m).
Raw AI measurement files are published at https://doi.org/10.5281/zenodo.6562764.
"meta" struct with meta information (recording data, laser power, pinhole size, used Minflux sequence, used dye and image concentration)