Result: Fluotracify - doctoral research project done in a reproducible way

This work is a collection of experiments about Fluorescence Correlation Spectroscopy (FCS) time-series artifacts. In multiple experiments, we simulated such artifacts, trained U-Net machine learning models to predict them, and found methods to optimize FCS time-series or Time-Correlated Single Photon Counting (TCSPC) data. This repository contains all code, most of the data, and interactive org-mode files describing the work I've done during my time in the Eggeling lab from January 2020 til Summer 2023 (after working on the same project since ~ April 2019). Connected paper and licenses If you use material from this repository, please cite the repository and the following paper: Seltmann, A.; Carravilla, P.; Reglinski, K.; Eggeling, E.; Waithe, D. Neural Network Informed Photon Filtering Reduces Artifacts in Fluorescence Correlation Spectroscopy Data. 2023 (currently under review) The nanosimpy module found under src/nanosimpy is a fork of Dominic Waithe's original nanosimpy library - here the original licensing applies. All software components (code) of this repository, e.g. the rest of the src directory, the data/mlruns directory, or python functions defined in the LabBook files, are licensed under the Apache-2.0 License - see the LICENSE file for details. All non-software components of this repository, e.g. plots, figures, correlated FCS files, reports on correlation fits, and the non-software components of the LabBooks, are licensed under a Creative Commons Attribution 4.0 International License - see the LICENSE-CC-BY file for details. Quickly viewing experiments Quickly view a rendered version of the full LabBook here. Getting started Viewing the electronic LabBook on Github The .org files can be viewed with markdown-like rendering here on Github. Github is not rendering the full information of these files yet, this is why displaying the raw file is recommended. Note that the file looks different depending on the branch you are on. The main branch does only include a barebones file without experiments, the ...