imagej_mosaic_ashlar.py

# @File(label="Select a slide to process") filename
# @File(label="Select the output location", style="directory") output_dir
# @String(label="Experiment name (base name for output files)") experiment_name
# @Integer(label="Rows", value=10) rows
# @Integer(label="Columns", value=10) cols

# Takes a slide (or other multi-series BioFormats-compatible file set) and
# generates flat- and dark-field correction profile images with BaSiC. The
# output format is two multi-series TIFF files (one for flat and one for dark)
# which is the input format used by Ashlar.

# Invocation for running from the commandline:
#
# /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run 
# imagej_mosaic_ashlar.py "filename='input.ext',output_dir='output',
# experiment_name='my_experiment',rows='10',cols='10'"

import sys
from ij import IJ, WindowManager
import ij.plugin.MontageMaker as MM
import ij.process.StackProcessor as StackProc
from ij.macro import Interpreter
from loci.plugins import BF
from loci.plugins.in import ImporterOptions


def main():

    Interpreter.batchMode = True

    print "Loading images..."

    options = ImporterOptions()
    options.setId(str(filename))
    options.setOpenAllSeries(True)
    options.setConcatenate(True)
    options.setSplitChannels(True)
    imps = BF.openImagePlus(options)

    num_channels = len(imps)
    w = imps[0].getWidth()
    h = imps[0].getHeight()

    for channel, imp in enumerate(imps):
        title = imp.getTitle()
        print "Processing:", title
        x, y, c, z, t = imp.getDimensions()
        assert z == 1 and c == 1
        imp.setDimensions(1, t, 1)

		# Generate thumbnail for cycle_offset measurement		
        mosaic_channel = 0
        if channel == mosaic_channel:
            StackProc(imp.getStack()).flipVertical()
            mosaic = MM().makeMontage2(
                imp, cols, rows, 0.1, 1, t, 1, 0, False
            )
            mosaic.getProcessor().flipVertical()
            mosaic_filename = '%s/%s-mosaic_c%s.tif' % (output_dir, experiment_name, mosaic_channel)
            IJ.saveAsTiff(mosaic, mosaic_filename)

        imp.close()

    print "Done!"


main()