brighteyes-flism 0.10.5

A toolbox for analysing FLISM images

BrightEyes-FLISM

Installation

Install brighteyes-flism from PyPI:

pip install brighteyes-flism

You can also install the latest development version directly from GitHub:

pip install git+https://github.com/VicidominiLab/BrightEyes-Flism

In case of local development:

git clone https://github.com/VicidominiLab/BrightEyes-Flism.git
cd BrightEyes-Flism
pip install -e .

brighteyes_flim re-exports the fitting and calibration helpers from brighteyes_mcs_file, including the optional model_fn, p0, bounds, and parameter_names arguments for custom multi-parameter fit models. This includes perform_fit_data, fit_data_with_ref_or_irf, calibrate_h5_file, and generate_fit_maps.

The HDF5 helpers understand the BrightEyes MCS 0.0.6 layout, including /raw/spad, /raw/aux, /calibration/results/<product>/..., and grouped virtual channels under /output/virtual_channels/<kind>/channel_<index>. Use load_raw(...) for current raw payloads and load_virtual_channel(...) for grouped virtual channels. They keep reader support for older raw acquisition files with root-level data and data_channels_extra datasets.

For plotting calibrated files, use load_calibration_summary(...) and load_calibration_fit_traces(...) instead of hard-coding calibration paths.