Multiparameter-based photosynthetic state transitions of single phytoplankton cells data

Dataset for Multiparameter-based photosynthetic state transitions of single phytoplankton cells data.

Creating environment

yaml and spec file are provided of the conda environment used. Most packages are typical, with the key exception of fretbursts

A custom/development version of fretbursts was used, which contains support for more flexible photon selection (Ph_sel) objects, necessary for the larger parameter space. This version is in the polarization branch of harripd fork of fretbursts. The simple route to install is 

pip install git+https://https://github.com/harripd/FRETBursts@polarization

however, if you want to ensure the exact same version is installed use:

pip install git+https://github.com/harripd/FRETBursts@12a5168

Data organization

All zip files are meant to be unziped into the same destination folder (ie if a file is in a folder in the zip file, it should be in a subfolder inside the shared highest level folder, but if two files inside different zip folders are in the root of their respective zip files, they should be places in the same folder when all files are unzipped.

After unzipping everything your folder for this article should contain the following items (normal text indicates file, bold text indicates folder).

Flow_API_all.ipynb

mpAlgae

figures

20230905_cyanoWH8102_diurnal

20230707_cyanolightjump

20230609_ppurp

20230724_redalgaelightjump

20231211_pmicans_6umol_diurnal

20231217_pmicans_6umol_lightjump

20231019_WH8102_imaging

bulk_cyano_lightjump

synWH8102_di_REPO_20230905.hdf5

synWH8102_di_REPO_20230905.csv

synWH8102_lj_REPO_20230707.hdf5

synWH8102_lj_REPO_20230707.csv

ppurp_di_REPO_20230609.hdf5

ppurp_di_REPO_20230609.csv

ppurp_lj_REPO_20230724.hdf5

ppurp_lj_REPO_20230724.csv

pmicans_di_REPO_20231211.hdf5

pmicans_di_REPO_20231211.csv

ppurp_lj_REPO_20230724.hdf5

ppurp_lj_REPO_20230724.csv

Flow_API_all.ipynb (item 1) is the jupyter notebook that analyses the data and produces the figures. It relies on having mpAlgae (item 2) in the same folder, as it contains the underlying code that adapts FRETBurts to work with the cell based data, adding functionality to combine multiple data files into one experiment, dynamic gating of data, storing calculated values to disk, which also reduces the memory requirements of the system, as well as a number of advanced plotting functions. Flow_API_all.ipynb also expects a figures folder (item 3) to exist so that it can save the produced figures. It also expects items 4-9 to exist, as those folder names are recorded as where the different raw data sets are stored. Even numbered items 12-22 (all items 12-23 that are hdf5 files) are produced by Flow_API_all.ipynb, and are where processed values of burst search are stored. the mpAlgae api makes it so that if these files are present, burst search is skipped, and instead loaded from these result files. Thus if you desire to examine the data, you only need the top level hdf5 files. These files also save results of histogram fittings, so that results can be loaded instead of recalculatd. 

The csv files are export of calculated parameters to csv format. Note that these are ungated, and thus proper gating must be implemented if plots are to be recapitulated from these files, this is done so that alternative gating strategies can also be explored.