def liveDead(row, f):
path, name = os.path.split(f)
img = ogre.site_to_array(f)
b = img[:, :, 0] # DAPI
g = img[:, :, 1] # FITC
r = img[:, :, 2] # TexasRed
bc = ogre.correct_illumination(b)
bcmask = ogre.adapt_thresh(bc)
blabs, bprops = ogre.watershed_label(bcmask, bc)
gc = ogre.correct_illumination(g)
gcmask = ogre.adapt_thresh(gc)
glabs, gprops = ogre.watershed_label(gcmask, gc)
rc = ogre.correct_illumination(r)
rcmask = ogre.adapt_thresh(rc)
rlabs, rprops = ogre.watershed_label(rcmask, rc)
# fig, ax = plt.subplots(3,3, figsize=(15,12))
# fig.suptitle(f, fontsize=15)
# ax[0,0].imshow(bc, cmap=plt.cm.gray)
# ax[0,1].imshow(gc, cmap=plt.cm.gray)
# ax[0,2].imshow(rc, cmap=plt.cm.gray)
# ax[1,0].imshow(bcmask, cmap=plt.cm.gray)
# ax[1,1].imshow(gcmask, cmap=plt.cm.gray)
# ax[1,2].imshow(rcmask, cmap=plt.cm.gray)
# ax[2,0].imshow(label2rgb(blabs))
# ax[2,1].imshow(label2rgb(glabs))
# ax[2,2].imshow(label2rgb(rlabs))
# sns.despine()
# fig.tight_layout()
# Raw cell counter seems to be doing a better job here...
raw_dapi = ogre.count_raw(bprops)
# bcount_filter = ogre.count_filter(bprops)
raw_fitc = ogre.count_raw(gprops)
# gcount_filter = ogre.count_filter(gprops)
raw_texas = ogre.count_raw(rprops)
# rcount_filter = ogre.count_filter(rprops)
glabmask = glabs != 0
rlabmask = rlabs != 0
live = 0
dead = 0
dying = 0
for i in range(1, blabs.max()):
nucleus_roi = blabs == i
if ((nucleus_roi * glabmask * rlabmask).any()):
dying += 1
elif ((nucleus_roi * glabmask).any()):
live += 1
elif ((nucleus_roi * rlabmask).any()):
dead += 1
return (row,
[path, name, raw_dapi, raw_fitc, raw_texas, live, dead, dying])
def liveDead(row, f):
path, name = os.path.split(f)
img = ogre.site_to_array(f)
b = img[:, :, 0] # DAPI
g = img[:, :, 1] # FITC
r = img[:, :, 2] # TexasRed
bc = ogre.correct_illumination(b)
bcmask = ogre.adapt_thresh(bc)
blabs, bprops = ogre.watershed_label(bcmask, bc)
gc = ogre.correct_illumination(g)
gcmask = ogre.adapt_thresh(gc)
glabs, gprops = ogre.watershed_label(gcmask, gc)
rc = ogre.correct_illumination(r)
rcmask = ogre.adapt_thresh(rc)
rlabs, rprops = ogre.watershed_label(rcmask, rc)
# fig, ax = plt.subplots(3,3, figsize=(15,12))
# fig.suptitle(f, fontsize=15)
# ax[0,0].imshow(bc, cmap=plt.cm.gray)
# ax[0,1].imshow(gc, cmap=plt.cm.gray)
# ax[0,2].imshow(rc, cmap=plt.cm.gray)
# ax[1,0].imshow(bcmask, cmap=plt.cm.gray)
# ax[1,1].imshow(gcmask, cmap=plt.cm.gray)
# ax[1,2].imshow(rcmask, cmap=plt.cm.gray)
# ax[2,0].imshow(label2rgb(blabs))
# ax[2,1].imshow(label2rgb(glabs))
# ax[2,2].imshow(label2rgb(rlabs))
# sns.despine()
# fig.tight_layout()
# Raw cell counter seems to be doing a better job here...
raw_dapi = ogre.count_raw(bprops)
# bcount_filter = ogre.count_filter(bprops)
raw_fitc = ogre.count_raw(gprops)
# gcount_filter = ogre.count_filter(gprops)
raw_texas = ogre.count_raw(rprops)
# rcount_filter = ogre.count_filter(rprops)
glabmask = glabs != 0
rlabmask = rlabs != 0
live = 0
dead = 0
dying = 0
for i in range(1, blabs.max()):
nucleus_roi = blabs == i
if((nucleus_roi * glabmask * rlabmask).any()):
dying += 1
elif((nucleus_roi*glabmask).any()):
live += 1
elif((nucleus_roi * rlabmask).any()):
dead += 1
return (row, [path, name, raw_dapi, raw_fitc, raw_texas, live, dead, dying])
for f in w1_files:
row = w1_files.index(f)
path, name = os.path.split(f)
print "Status Update:"
print "File: {0}".format(f)
print "Item: {0}/{1}".format(row, w1_files_length)
img = ogre.site_to_array(f)
b = img[:, :, 0] # DAPI
g = img[:, :, 1] # FITC
r = img[:, :, 2] # TexasRed
bc = ogre.correct_illumination(b)
bcmask = ogre.adapt_thresh(bc)
blabs, bprops = ogre.watershed_label(bcmask, bc)
gc = ogre.correct_illumination(g)
gcmask = ogre.adapt_thresh(gc)
glabs, gprops = ogre.watershed_label(gcmask, gc)
rc = ogre.correct_illumination(r)
rcmask = ogre.adapt_thresh(rc)
rlabs, rprops = ogre.watershed_label(rcmask, rc)
# fig, ax = plt.subplots(3,3, figsize=(15,12))
# fig.suptitle(f, fontsize=15)
# ax[0,0].imshow(bc, cmap=plt.cm.gray)
# ax[0,1].imshow(gc, cmap=plt.cm.gray)
# ax[0,2].imshow(rc, cmap=plt.cm.gray)
for f in w1_files:
row = w1_files.index(f)
path, name = os.path.split(f)
print "Status Update:"
print "File: {0}".format(f)
print "Item: {0}/{1}".format(row, w1_files_length)
img = ogre.site_to_array(f)
b = img[:, :, 0] # DAPI
g = img[:, :, 1] # FITC
r = img[:, :, 2] # TexasRed
bc = ogre.correct_illumination(b)
bcmask = ogre.adapt_thresh(bc)
blabs, bprops = ogre.watershed_label(bcmask, bc)
gc = ogre.correct_illumination(g)
gcmask = ogre.adapt_thresh(gc)
glabs, gprops = ogre.watershed_label(gcmask, gc)
rc = ogre.correct_illumination(r)
rcmask = ogre.adapt_thresh(rc)
rlabs, rprops = ogre.watershed_label(rcmask, rc)
# fig, ax = plt.subplots(3,3, figsize=(15,12))
# fig.suptitle(f, fontsize=15)
# ax[0,0].imshow(bc, cmap=plt.cm.gray)
# ax[0,1].imshow(gc, cmap=plt.cm.gray)
# ax[0,2].imshow(rc, cmap=plt.cm.gray)
