Data from: Single-protein optical holography

This repository contains the data and code necessary to reproduce the results presented in the paper "Single-protein optical holography" by JC Thiele, E Pfitzner, and P Kukura.
A preprint is available on bioRxiv: https://doi.org/10.1101/2023.08.14.552817

There are two folders:
- Code: The Python code to analyse the data and generate figures. The following files are included:
- fig1b_simulate_complex_image.py: Generate the illustration found in Figure 1b of the article.
- fig2_plot_panel.py: Generates the panel plot in Figure 2: camera images and intensity, amplitude, and phase time traces from detected particles in the 40 nm AuNP sample.
- fig5_plot_panel.py: Generates the panel plot in Figure 5: contrast distributions for AuNPs in holographic and darkfield measurements, calculation of the specific excess polarisability of proteins.
- analyse_AuNP_phaseramp.py: Analysis script to generate the "particle_fits_*.h5" used in Figure 2 and 5. Detection and fitting of immobilised particles for darkfield and phase-modulated holographic measurements.
- requirements.txt: list of Python dependencies
- Jupyter notebooks to analyse protein landing measurements.
- Data: The raw and analysed data stored as hdf5 files. The following data is included:
- 20 repeats of phase-shifting measurements of immobilised gold nanoparticles (20 nm, 40 nm, 60 nm). The files "darkfieldX.h5" contains the darkfield measurement from all for cameras. The file "phaseX.h5" contains the reference and interferometric measurement from the corresponding field of view while the phase delay in the sample path was modulated.
- In the folders of the nanoparticle measurement, "particle_fits_*.h5" are included containing the fit results (position, amplitude, phase, fit error) for the darkfield measurement (all cameras independently) and holographic measurements (for different focus positions and phase delays).
- In the folders of "DynDPRD landing events" the movies and analysed landing events can be found. The subfolder Movies, contains four protein landing measurements (termed "2ul_MS1000_xxx") from two days and the corresponding buffer, darkfield, and phase-shifting measurements. Note that all .h5 files contain prealigned and 2x2 binned data for all four phase shifted cameras. The subfolder Landning events contains the detected and fitted landing events used in Figure 3 and 4.