Fiji script: Crop and merge images by ROIs. Adds green and red colors to images with no LUT.

crop_and_merge2.py

from ij import IJ, ImagePlus, ImageStack
from ij.process import ColorProcessor, ImageConverter
from ij.plugin import ContrastEnhancer, ImageCalculator, StackCombiner
import csv

folder = "/Volumes/Macintosh HD/Google Drive/Groves/Scope 7/20141126 Immunostaining/"


def in_path(folder,num):
	return [folder + "01 FC4 of 1125/02 tirf and confocal/tirf_"+row[0]+"/Pos0/img_000000000_488tirf_100x_000.tif",
			folder + "01 FC4 of 1125/02 tirf and confocal/tirf_"+row[0]+"/Pos0/img_000000000_561tirf_100x_000.tif"]
	

def out_path(folder,count):
    return [folder+"01B 02 tirf/out_"+str(count)+"_488.tiff",
    		folder+"01B 02 tirf/out_"+str(count)+"_561.tiff",
    		folder+"01B 02 tirf/out_"+str(count)+"_merge.tiff"]


# Crop a single image
def crop(imp,x,y,w,h):
    imp.setRoi(x,y,w,h)
    ip = imp.getProcessor()
    return ip.crop(),imp


# Return a cropped ImagePlus, color added, contrast adjusted.
def process_channel(imp,x,y,w,h,color,title):
    cr,o = crop(imp,x,y,w,h);
    imc = ImagePlus(title,cr)
    ContrastEnhancer().stretchHistogram(imc,0.35)
    IJ.run(imc,color,"")
    return imc


def combine_multiple(w,h,imp):
    res = ImageStack(w,h)
    res.addSlice(imp[0].getProcessor())
    for im in imp[1:]:
        st = ImageStack(w,h)
        st.addSlice(im.getProcessor())
        res = StackCombiner().combineHorizontally(res,st)
    return res


def process(count,imp,imp2,x,y,w,h):
    f1,f2,f3 = out_path(folder,count)
    crop488 = process_channel(imp,x,y,w,h,'Green','488')
    IJ.save(crop488,f1)
    crop561 = process_channel(imp2,x,y,w,h,'Red','561')
    IJ.save(crop561,f2)

	# Make a combined image of 488, 561, and merged.
    ImageConverter(crop488).convertToRGB()
    merge = ImageCalculator().run("Add create", crop488,crop561);
    three = combine_multiple(w,h,[crop488,crop561,merge])
    IJ.save(ImagePlus("merge",three),f3)


def get_images(path):
	return IJ.openImage(path[0]), IJ.openImage(path[1])


# Assume the CSV file has five columns: file id, x, y, width, height
infile = folder + '01B rois.csv'
csvfile = open(infile, 'rU')
maxProcess = 1000

try:
    # reader is used for reading a csv line by line.
    reader = csv.reader(csvfile)
    # Skip the title row
    reader.next()
    
    count = 0
    prev = None
    imp = None
    
    for row in reader:
        if len(row) >= 5:
            count += 1
            if count > maxProcess:
               break
            if prev != row[0]:
#				 This macro does not open files in GUI, and the line below is not needed.
#                IJ.run('Close All')
                path = in_path(folder,row[0])
                print(path[0])
                imp, imp2 = get_images(path)
            prev = row[0]
            process(count, imp, imp2, *map(int, row[1:5]))
            print(count)
            
# finally block is executed in the end no matter if an error occurs or not.
finally:
    csvfile.close()
#    IJ.run('Close All')