Plots kerr plots and analyzes results generated by the NAA GECI analysis code. Allows for spot-checking raw image data and movies.

Ilya Kolb
Janelia Research Campus
Howard Hughes Medical Institute
kolbi@janelia.hhmi.org

This code is dependent on outputs from the NAA_analysis workflow, namely, the Excel spreadsheets such as data_week_XXXXXXX_GCaMP96uf_raw_GCaMP96uf.xlsx and compiled data such as pile_week_GCaMP96uf_upto_20200310_GCaMP96uf_raw.mat

• MATLAB 2019a+
• Access to dm11:/genie/GECIScreenData/Analysis (analyzed data from GECI screen)
• Fiji (if running from the script)

1. Download the fastGCaMP_analysis directory to your computer
2. Add fastGCaMP_analysis/accessory_funcs to MATLAB path

1. Open kerr_plot_CGaMP96uf.m in MATLAB. Set the good variable to point to the data_all or data_week xlsx file e.g. in dm11:\GECIScreenData\Analysis
2. Set the variables to plot (xToPlot, yToPlot, etc) according to the field names in the good table
3. To plot averaged traces of hit constructs, run compare_constructs_GCaMP96uf.m.

• In the 'hits' cell array, put in mutant names you want to look at (e.g. '500.333')
• In the 'control' field, set the name of the control (e.g. '10.921' for jGCaMP7f)
• Set 'plotRaw' to 1 if you want to plot individual responses from wells in each constructs. Also set numSampleWells to limit how many wells per construct will be plotted.
• Set launchFiji to 1 to automatically launch Fiji from the plotRawCellData script. Only happens if plotRaw is set to 1.
• See specific instructions in compare_constructs_GCaMP96uf.m for details on other parameters

• Remember to set hardcoded directories in plotRawCellData.m.
• launchFiji can be buggy