jandoG

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

jandoG

from ij import IJ, ImagePlus
from ij.gui import Roi
from ij.plugin.filter import ParticleAnalyzer as PA
from ij.measure import Measurements, ResultsTable
from ij.plugin.frame import RoiManager

def getRoisByParticleAnalysis(mask, measures, minsize=0.01, maxsize=100.0, mincirc=0.1, maxcirc=1.0):
	"""
	Function to get array of rois from input mask.
	Input: