This code is a reimagining of

Robert Staadt

Development of a system for high-volume multi-channel brain imaging of fluorescent voltage signals

Dissertation

Ruhr-Universität Bochum, Universitätsbibliothek

08.02.2024

https://doi.org/10.13154/294-11032

---

Updated: 19.03.2025

Files are now organized in subdirectories to distinguish better between code for GEVI or GECI analysis.

gevi-geci/ stage_1*, stage_2*, stage_3*, stage_4*, stage_5* -> main stages for data preprocessing -> use e.g.: python stage_1_get_ref_image.py -c config_example_GEVI.json functions/ -> functions used by the main stages

gevi-geci/gevi/ config_example_GEVI.json -> typical config file for GEVI (compare to gevi-geci/geci/config_example_GECI.json) config_M0134M*, config_M3905F* -> config files for a few recordings (adjust directory names, if necessary!) example_load_gevi.py -> simple script demonstrating how to load data

gevi-geci/geci/ config_example_GECI.json -> typical config file for GECI (compare to gevi-geci/gevi/config_example_GEVI.json) config_M_Sert_Cre_4* -> config files for a few recordings (adjust directory names, if necessary!) stage_6_convert_roi.py -> additional stage for the analysis of Hendrik's recordings -> use e.g.: python stage_6_convert_roi.py -f config_M_Sert_Cre_41.json geci_loader.py, geci_plot.py -> additional code for summarizing the results and plotting with the ROIs -> use e.g. python geci_loader.py --filename config_M_Sert_Cre_41.json

gevi-geci/other/ stage_4b_inspect.py, stage_4c_viewer.py -> temporary code for assisting search for implantation electrode