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Run "01downsizedMovie.py" Select experiment folder Hatching timepoint can be set to 0 if not needed Let the script run overnight to generate all the movie for all channels needed
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For each worm, open the coolLED movie with imagej In a txt file called skin.txt, annotate hatching time, and timepoints in which skin appears (L2 and L3) Timepoints are as shown by imagej - 1 (compare skin files already present)
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Run "02markGoand.py" Select the _analyzedImages folder Annotate the gonad position starting from 5 hours before L2 (time shown on top-left corner of the image) NOTE: once clicked, the figure automatically shows the next image, mouse wheels manually goes to next/previous timepoint, right click removes the gonad position of current timepoint NOTE: the gonad pos at the current timepoint is not saved, so you need to move to next or previous timepoint before clicking the save button
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Run "03cropImages.py" Select experiment folder Let the script run overnight NOTE: When done, the raw data can be deleted!
04 Run "04markCells.py" Manually annotate the timepoint in which cells divide and the ID of the AC by looking at images by eye Annotate data in "birthOrderToOutcome.txt" file (compare txt files already existing)
05 Run "10histoBirthOrderVSOutcome" to generate figure of 1st born/2nd born = AC NOTE: folders with experimental data are hardcoded. Change it to include more data if running more experiments.
06 Run "04markCells.py" Label cells and background in every timepoint possible, ending at L3 molt Save data
07 Run "09cellsMovie.py" experimental folder is hardcoded!
08 Run "15quickAndDirtyFluoCompute.py" experimental folder is hardcoded!
09 Run "16quickAndDirtyFluoPlot", "16quickAndDirtyRatioPlot" to visualize data Run "histoTimeToDecide_q&d" to look at time to decision All these scripts are hard coded
10 To make life easier, run "CreatSingleFileWithAllData" to generate flitered trajectories and store raw and filtered fluorescence data in a single list NOTE: The object is not pickled anywhere, manually use pickle.dump to store it anywhere you like
11 Use "q&dAbsPlot_test", "q&dRatioHist_test", "q&dRatioPlot_test", "q&dTdec_test" to make all the plots discussed above in a much faster way with the singleFile created at point 10 NOTE: you need to specify the location of the file to load!