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)
- Download the
fastGCaMP_analysis
directory to your computer - Add
fastGCaMP_analysis/accessory_funcs
to MATLAB path
- Open
kerr_plot_CGaMP96uf.m
in MATLAB. Set thegood
variable to point to thedata_all
ordata_week
xlsx file e.g. indm11:\GECIScreenData\Analysis
- Set the variables to plot (
xToPlot
,yToPlot
, etc) according to the field names in thegood
table - 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