# source_directory = "L:\\Common\\AKN\\IF test images nuc vs cyto\\11-21-16 RPE IF untreat mps nut images" # because Windows
# source_directory = "C:\\Users\\Andrei\Desktop\\tmp\\11-21-16 RPE IF untreat mps nut images" # because windows and smb are not collaborating today
# source_directory = "C:\\Users\Gordon\Desktop\AKN_TIFF 8BIT"
source_directory = "D:\AKN_TIFF 8BIT"
# source_directory = "D:\AKN_TIFF_16"
# source_directory = "D:\AKN_TIFF_TEST"
pipeline = uf.color_based_traversal(source_directory,
coding_separator='.',
group_anchor=1)
pipeline = uf.name_channels(pipeline, ['transmission', 'DAPI', 'p53'])
print "1"
pipeline = wf.gamma_stabilize(pipeline,
in_channel='DAPI',
floor_method='min',
alpha_clean=.5)
pipeline = wf.smooth_2d(pipeline, in_channel='DAPI',
smoothing_px=.5) # corresponds to a pixel of 1500 nm
print "2"
pipeline = wf.gamma_stabilize(pipeline,
in_channel='p53',
floor_method='min',
alpha_clean=.0)
pipeline = wf.smooth_2d(pipeline, in_channel='p53', smoothing_px=.5)
print "3"
pipeline = wf.robust_binarize(pipeline,
in_channel='DAPI',
out_channel=['nuclei'],
import imagepipe.wrapped_functions as wf
from imagepipe import core_functions as cf
translator = {'C2': 0,
'C1': 1
}
source = examples.xi_support.xi_traverse('L:\\Users\\xi\\Quantification of colocalization',
matching_map=translator)
# source = uf.xi_traverse('L:\\Users\\andrei\\2017\\Xi Data',
# matching_map=translator)
named_source = uf.name_channels(source, ['GFP', 'mCherry'])
stabilized_GFP = wf.gamma_stabilize(named_source, in_channel='GFP', floor_method='min', alpha_clean=.5)
smoothed_GFP = wf.smooth(stabilized_GFP, in_channel='GFP', smoothing_px=.5)
stabilized_mCh = wf.gamma_stabilize(smoothed_GFP, in_channel='mCherry', floor_method='min', alpha_clean=.5)
smoothed_mCh = wf.smooth(stabilized_mCh, in_channel='mCherry', smoothing_px=.5)
med_norm_GFP = wf.locally_normalize(smoothed_mCh,
in_channel='GFP',
)
med_norm_mCh = wf.locally_normalize(med_norm_GFP,
in_channel='mCherry',
)
source = examples.kristen_support.Kristen_traverse(
'/run/user/1000/gvfs/smb-share:server=10.17.0.219,share=common/Users/kristen/Split GFP quant_Andrei/20170209',
matching_map=translator)
named_source = uf.name_channels(source, ['DAPI', 'GFP', 'mCherry'])
max_mCherry = wf.max_projection(named_source,
in_channel='mCherry',
out_channel='max_mCherry')
max_GFP = wf.max_projection(max_mCherry,
in_channel='GFP',
out_channel='max_GFP')
stabilized_mCherry = wf.gamma_stabilize(max_GFP,
in_channel='max_mCherry',
floor_method='min',
alpha_clean=.5)
smoothed_mCherry = wf.smooth_2d(stabilized_mCherry,
in_channel='max_mCherry',
smoothing_px=.5)
mCherry_o_n_segmented = wf.robust_binarize(smoothed_mCherry,
in_channel='max_mCherry',
out_channel='max_mCherry_binary',
heterogeity_size=10,
feature_size=250)
running_render = examples.kristen_support.Kristen_render(
mCherry_o_n_segmented,
in_channel=[
translator = {'w1488': 0, 'w2561': 1}
# source = uf.Linhao_traverse("L:\\Users\\jerry\\Image\\ForAndrei\\Ry233282285",
# matching_map=translator)
source = examples.linhao_support.Linhao_traverse(
"/run/user/1000/gvfs/smb-share:server=10.17.0.219,share=common/Users/jerry/Image/ForAndrei/SSAmutant",
matching_map=translator)
# that architecture actually removes the need for the debug line
# that can be incorporated into the traversal
named_source = uf.name_channels(source, ['GFP', 'mCherry'])
stabilized_GFP = wf.gamma_stabilize(named_source, in_channel='GFP')
smoothed_GFP = wf.smooth(stabilized_GFP, in_channel='GFP')
stabilized_mCh = wf.gamma_stabilize(smoothed_GFP, in_channel='mCherry')
projected_GFP = wf.sum_projection(stabilized_mCh,
in_channel='GFP',
out_channel='projected_GFP')
projected_mCh = wf.max_projection(projected_GFP,
in_channel='mCherry',
out_channel='projected_mCh')
binarized_GFP = wf.robust_binarize(projected_mCh,
in_channel='projected_mCh',
out_channel='cell_tags')
import examples.akshay_support
import imagepipe.traversals as uf
import imagepipe.wrapped_functions as wf
from imagepipe import core_functions as cf
# source = uf.Akshay_traverse("L:\\Common\\AKN\\IF test images nuc vs cyto\\tiff")
# source = uf.Akshay_traverse("L:\\Common\\AKN\\IF test images nuc vs cyto\\11-21-16 RPE IF untreat mps nut images")
# source_directory = '/run/user/1000/gvfs/smb-share:server=10.17.0.219,share=common/Common/AKN/IF test images nuc vs cyto/11-21-16 RPE IF untreat mps nut - Analysis run' # because Linux
source_directory = "L:\\Common\\AKN\\IF test images nuc vs cyto\\11-21-16 RPE IF untreat mps nut images" # because Windows
# source_directory = "C:\\Users\\Andrei\Desktop\\tmp\\11-21-16 RPE IF untreat mps nut images" # because windows and smb are not collaborating today
source = examples.akshay_support.Akshay_traverse(source_directory)
named_source = uf.name_channels(source, ['DAPI', 'p53', 'p21'])
stablilized_1 = wf.gamma_stabilize(named_source, in_channel='DAPI', floor_method='min', alpha_clean=.5)
smoothed_1 = wf.smooth_2d(stablilized_1, in_channel='DAPI', smoothing_px=.5) # corresponds to a pixel of 1500 nm
stablilized_2 = wf.gamma_stabilize(smoothed_1, in_channel='p53', floor_method='min', alpha_clean=.0)
smoothed_2 = wf.smooth_2d(stablilized_2, in_channel='p53', smoothing_px=.5)
stablilized_3 = wf.gamma_stabilize(smoothed_2, in_channel='p21', floor_method='5p', alpha_clean=.5)
smoothed_3 = wf.smooth_2d(stablilized_3, in_channel='p21', smoothing_px=.5)
binarized_nuclei = wf.robust_binarize(smoothed_3,
in_channel='DAPI',
out_channel=['nuclei'],
_dilation=0,
heterogeity_size=5, feature_size=50)
segmented_nuclei = wf.label_and_correct(binarized_nuclei,