Open images using bio-formats API (run with FIJI)

fiji_jython_bioformats_example.py

from ij import IJ, ImagePlus
from loci.plugins import BF
from loci.formats import ImageReader, FilePattern
from loci.formats import MetadataTools
from loci.plugins.prefs import OptionsList
from loci.plugins.in import ImporterOptions

def openImageWithBF(path, virtual= True, groupfiles = False, seriesdata = False, openseries = 1):
	"""
	set options to open image using bio-formats- use virtual for quick loading
	params:
	path to file 
	virtual: bool set True to load image as virtual stack (for big data)
	groupfiles: bool set True to load images from folder having similar name pattern (stored in the metadata of first image)
	seriesdata: bool set True if image contains series 
	openseries: int series ID no to be opened 
	returns: 
	imp: ImagePlus 
	"""
	options = ImporterOptions()
	options.setColorMode(ImporterOptions.COLOR_MODE_DEFAULT)
	options.setAutoscale(True)
	options.setStackFormat("Hyperstack")
	options.setVirtual(virtual)
	options.setGroupFiles(groupfiles) 
	
	if seriesdata: 
		reader = ImageReader()
		reader.setId(path)
		seriesCount = reader.getSeriesCount()
		reader.close()
		print "Found series data. Image series count =", seriesCount
		print "Reading series ID ", openseries, "\n"
		options.setOpenAllSeries(True)

	options.setId(path)
	allimps = BF.openImagePlus(options)

	if seriesdata:
		imp = allimps[openseries - 1]

	else:
		imp = allimps[0]
	
	return imp
	
imagepath = "C:\Users\Gaya\test.czi"
imp = openImageWithBF(imagepath, virtual= True)
imp.show()