annotateWorm.m -	1) find points of interest (POI, in my case nuclei of VPCs)
			2) find region of interest (ROI, in my case the area in the worm where the VPCs are)
			3) find gonad axis

	subroutines:		output:

	getPOI.m		POI*.mat
	getVPC_ROI.m		VPC_ROI*.mat
	getGonadAxis.m		gonadAxis*.mat

findMRNA.m - 	find all mRNA spots and assign them to the correct VPC/Pn.p cell.

	subroutines:		output:
	
	filterSpotData.m	filteredSpotData*.mat
	getThresholds.m		spotThresholds*.mat
	findSpots.m		spotCoordinates*.mat
	getMRNAperVPC.m		VPC_mRNA*.mat
	
combineWormData.m -	Calculates a number of properties for the data set described in the input file:
			1) Calculate mRNA vs gonad length (saved as <scatterMRNA> and <avgMRNA>)
			2) Calculate average mRNA in each cell in all lineages binned for gonad length (saved as <Pnp>)

	output: <inputFileName>.mat

makeCombinedDataFigure.m -	Example of plotting 1) mRNA vs gonad length and 2) average mRNA in each cell in all lineages

	subroutine: construct2DmRNAfig.m (for plotting mRNA in individual cells binnen for gonad length)

Example input file <lin-12.input>:

name    Lin-12
root    E:\Jeroen
path    8-5-2009\lin-12_A592_lag-2_Cy5_26-40hrs_batch1
channel 1
Lbins   200 100 1500
Pnp     20 600 700 8000
Pnpx    80 900 1000 11000
Pnpxx   110 1200 1300 14000