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59 lines
1.8 KiB
Markdown
59 lines
1.8 KiB
Markdown
This code is a reimagining of
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Robert Staadt
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Development of a system for high-volume multi-channel brain imaging of fluorescent voltage signals
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Dissertation
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Ruhr-Universität Bochum, Universitätsbibliothek
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08.02.2024
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[https://doi.org/10.13154/294-11032](https://doi.org/10.13154/294-11032)
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Updated: 19.03.2025
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Files are now organized in subdirectories to distinguish better between code for GEVI or GECI analysis.
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gevi-geci/
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stage_1*, stage_2*, stage_3*, stage_4*, stage_5*
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-> main stages for data preprocessing
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-> use e.g.: python stage_1_get_ref_image.py -c config_example_GEVI.json
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functions/
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-> functions used by the main stages
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gevi-geci/gevi/
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config_example_GEVI.json
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-> typical config file for GEVI (compare to gevi-geci/geci/config_example_GECI.json)
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config_M0134M*, config_M3905F*
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-> config files for a few recordings (adjust directory names, if necessary!)
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example_load_gevi.py
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-> simple script demonstrating how to load data
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gevi-geci/geci/
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config_example_GECI.json
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-> typical config file for GECI (compare to gevi-geci/gevi/config_example_GEVI.json)
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config_M_Sert_Cre_4*
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-> config files for a few recordings (adjust directory names, if necessary!)
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stage_6_convert_roi.py
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-> additional stage for the analysis of Hendrik's recordings
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-> use e.g.: python stage_6_convert_roi.py -f config_M_Sert_Cre_41.json
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geci_loader.py, geci_plot.py
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-> additional code for summarizing the results and plotting with the ROIs
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-> use e.g. python geci_loader.py --filename config_M_Sert_Cre_41.json
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gevi-geci/other/
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stage_4b_inspect.py, stage_4c_viewer.py
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-> temporary code for assisting search for implantation electrode
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