def setbfpath():
# specify bioformats_package.jar to use if required
bfpackage = r'bfpackage/5.4.1/bioformats_package.jar'
bf.set_bfpath(bfpackage)
return bfpackage
def ReadImage(filename):
urlnamespace = 'http://www.openmicroscopy.org/Schemas/OME/2016-06'
# specify bioformats_package.jar to use if required
bfpackage = r'c:\Users\M1SRH\Documents\Software\BioFormats_Package\5.4.1\bioformats_package.jar'
bf.set_bfpath(bfpackage)
# get image meta-information
MetaInfo = bf.get_relevant_metainfo_wrapper(filename, namespace=urlnamespace, bfpath=bfpackage, showinfo=False)
img6d, readstate = bf.get_image6d(filename, MetaInfo['Sizes'])
# show relevant image Meta-Information
bf.showtypicalmetadata(MetaInfo, namespace=urlnamespace, bfpath=bfpackage)
return img6d
if args.savefigure == 'True':
save = True
elif args.savefigure == 'False':
save = False
# get show surface options
if args.showsurface == 'True':
surface = True
elif args.showsurface == 'False':
surface = False
# specify bioformats_package.jar to use if required
# Attention: for larger CZI tile images containing an image pyramid one must still use 5.1.10
# since the latest version is not fully supported by python-bioformats yet
bfpackage = r'bfpackage/5.1.10/bioformats_package.jar'
bf.set_bfpath(bfpackage)
# create plane info from CZI image file and write CSV file (optional)
planetable, filenamecsv = bf.get_planetable(filenameczi,
writecsv=wcsv,
separator=separator)
# show the dataframe
print(planetable[:10])
# define name for figure to be saved
figuresavename = os.path.splitext(filenamecsv)[0] + '_XYZ-Pos' + '.' + saveformat
# display the XYZ positions
fig1, fig2 = bf.scatterplot(planetable,
ImageID=0,
def setbfpath():
# specify bioformats_package.jar to use if required
bfpath = r'c:\BioFormats_Package\5.1.9\bioformats_package.jar'
bf.set_bfpath(bfpath)
if args.savefigure == 'True':
save = True
elif args.savefigure == 'False':
save = False
# get show surface options
if args.showsurface == 'True':
surface = True
elif args.showsurface == 'False':
surface = False
# specify bioformats_package.jar to use if required
# Attention: for larger CZI tile images containing an image pyramid one must still use 5.1.10
# since the latest version is not fully supported by python-bioformats yet
bfpackage = r'bioformats_package_5_1_10.jar'
bf.set_bfpath(bfpackage)
# create plane info from CZI image file and write CSV file (optional)
planetable, filenamecsv, MetaInfo = bf.get_planetable(filenameczi,
writecsv=wcsv,
separator=separator,
showinfo=True)
# show the dataframe
print(planetable[:10])
# define name for figure to be saved
figuresavename = os.path.splitext(
filenamecsv)[0] + '_XYZ-Pos' + '.' + saveformat
# display the XYZ positions