Description of macros:

53BP1count.ijm:
	ImageJ macro for counting foci per nucleus, based on intensity maxima, in cells
	expressing a fluorescent protein construct.
	Input: Directory containing image stacks (10 images/channel) with the following channels:
			Channel 1: Expression marker (e.g. GFP-tagged rescue construct)
			Channel 2: Foci marker (e.g. 53BP1 antibody channel)
			Channel 3: Nuclear marker (e.g. DAPI)
	Output: Foci counts per nucleus (N.B. will need to adjust noise threshold based on background)

NCIntMeas.ijm:
	ImageJ macro for recording the total cellular and nuclear integrated fluorescence
	intensity for a given fluorescent protein.
	Input: Directory containing image stacks (12 images/channel) with the following channels:
			Channel 1: Tagged protein for which to measure nuclear/cytoplasmic intensities
			Channel 2: Nuclear marker (e.g. DAPI)
	Output: List of measurements, alternating between cytoplasmic area+intensity and
			nuclear area_intensity. (N.B. need to specify these measurements with "Set
			Measurements" before running macro)

getNCratio.py:
	Python script which calculates the nuclear/cytoplasmic intensity ratio (per pixel)
	based on the output of NCIntMeas.imj
	Input: ImageJ measurement file (tab-delimited).
	Output: (i) List of calculated values for cytoplasmic area, cytoplasmic intensity,
	       cytoplasmic concentation, nuclear area, nuclear intensity, nuclear concentration
	       for each cell (can export to Excel). (ii) Sum of nuclear concentration/cytoplasmic 
	       concentration for all cells. 

RO2measure_single.ijm:
	ImageJ macro for calculating the ratio of (background-subtracted) intensities for two
	channels. 
	Input: Single two-channel image (not a stack), e.g. roGFP2-NLS emission after excitation
		   at two different wavelengths. The macro is run on each file individually, and
		   the area in which to calculate the ratio (e.g. the nucleus) is selected by hand.
	Output:	Integrated intensity ratio and area within hand-selected ROI.
			
