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fiji_script_vertical_combination.py
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Created
Tue, Jun 11, 15:05
Size
4 KB
Mime Type
text/x-objective-c
Expires
Thu, Jun 13, 15:05 (2 d)
Engine
blob
Format
Raw Data
Handle
18244654
Attached To
R6289 Motion correction paper
fiji_script_vertical_combination.py
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#@String parameter_file
#@Integer lmbd
#@Integer gamma
from
ij
import
IJ
,
ImagePlus
from
ij.io
import
Opener
,
FileSaver
from
ij.plugin
import
RGBStackMerge
,
StackCombiner
,
Resizer
from
ij.process
import
ImageConverter
from
ij.plugin
import
Resizer
,
ZProjector
,
ImageCalculator
import
sys
import
json
#import file paths
json_file
=
open
(
parameter_file
,
'r'
)
text
=
json_file
.
read
()
files
=
json
.
loads
(
text
)
json_file
.
close
()
#Instanciate necessary classes
opener
=
Opener
()
RGB_stack_merge
=
RGBStackMerge
()
stack_combiner
=
StackCombiner
()
resizer
=
Resizer
()
ic
=
ImageCalculator
()
z_proj
=
ZProjector
()
print
(
'Processing lambda={} gamma={}'
.
format
(
lmbd
,
gamma
))
outdir
=
files
[
'output_dir'
]
+
'/l{}g{}'
.
format
(
lmbd
,
gamma
)
#Open images
unregistered_GC6s_info
=
opener
.
getTiffFileInfo
(
files
[
'output_dir'
]
+
'/GC6s_preprocessed.tif'
)
unregistered_GC6s_imp
=
opener
.
openTiffStack
(
unregistered_GC6s_info
)
unregistered_tdTom_info
=
opener
.
getTiffFileInfo
(
files
[
'output_dir'
]
+
'/tdTom_preprocessed.tif'
)
unregistered_tdTom_imp
=
opener
.
openTiffStack
(
unregistered_tdTom_info
)
registered_GC6s_info
=
opener
.
getTiffFileInfo
(
outdir
+
'/warped2.tif'
)
registered_GC6s_imp
=
opener
.
openTiffStack
(
registered_GC6s_info
)
registered_tdTom_info
=
opener
.
getTiffFileInfo
(
outdir
+
'/warped1.tif'
)
registered_tdTom_imp
=
opener
.
openTiffStack
(
registered_tdTom_info
)
vector_info
=
opener
.
getTiffFileInfo
(
outdir
+
'/vectors.tif'
)
vector_imp
=
opener
.
openTiffStack
(
vector_info
)
#Convert fluorescence images to 32-bit and adjust brightness
IJ
.
run
(
unregistered_GC6s_imp
,
"32-bit"
,
"slices"
)
IJ
.
run
(
registered_GC6s_imp
,
"32-bit"
,
"slices"
)
IJ
.
run
(
unregistered_tdTom_imp
,
"32-bit"
,
"slices"
)
IJ
.
run
(
registered_tdTom_imp
,
"32-bit"
,
"slices"
)
IJ
.
run
(
unregistered_GC6s_imp
,
"Enhance Contrast"
,
"saturated=0.35"
);
IJ
.
run
(
registered_GC6s_imp
,
"Enhance Contrast"
,
"saturated=0.35"
);
IJ
.
run
(
unregistered_tdTom_imp
,
"Enhance Contrast"
,
"saturated=0.35"
);
IJ
.
run
(
registered_tdTom_imp
,
"Enhance Contrast"
,
"saturated=0.35"
);
IJ
.
run
(
vector_imp
,
"Enhance Contrast"
,
"saturated=0.35"
);
#Remove first frame from registered and unregistered stacks
IJ
.
run
(
unregistered_GC6s_imp
,
"Delete Slice"
,
""
)
IJ
.
run
(
registered_GC6s_imp
,
"Delete Slice"
,
""
)
IJ
.
run
(
unregistered_tdTom_imp
,
"Delete Slice"
,
""
)
IJ
.
run
(
registered_tdTom_imp
,
"Delete Slice"
,
""
)
#Upsample to resolution of vector image
IJ
.
run
(
unregistered_GC6s_imp
,
"Size..."
,
"width=
%d
height=
%d
depth=
%d
interpolation=None"
%
(
vector_imp
.
getWidth
(),
vector_imp
.
getHeight
(),
vector_imp
.
getStackSize
()))
IJ
.
run
(
registered_GC6s_imp
,
"Size..."
,
"width=
%d
height=
%d
depth=
%d
interpolation=None"
%
(
vector_imp
.
getWidth
(),
vector_imp
.
getHeight
(),
vector_imp
.
getStackSize
()))
IJ
.
run
(
unregistered_tdTom_imp
,
"Size..."
,
"width=
%d
height=
%d
depth=
%d
interpolation=None"
%
(
vector_imp
.
getWidth
(),
vector_imp
.
getHeight
(),
vector_imp
.
getStackSize
()))
IJ
.
run
(
registered_tdTom_imp
,
"Size..."
,
"width=
%d
height=
%d
depth=
%d
interpolation=None"
%
(
vector_imp
.
getWidth
(),
vector_imp
.
getHeight
(),
vector_imp
.
getStackSize
()))
#Rotate all images
IJ
.
run
(
unregistered_GC6s_imp
,
"Rotate..."
,
"angle=-90 grid=1 interpolation=Bilinear stack"
)
IJ
.
run
(
registered_GC6s_imp
,
"Rotate..."
,
"angle=-90 grid=1 interpolation=Bilinear stack"
)
IJ
.
run
(
unregistered_tdTom_imp
,
"Rotate..."
,
"angle=-90 grid=1 interpolation=Bilinear stack"
)
IJ
.
run
(
registered_tdTom_imp
,
"Rotate..."
,
"angle=-90 grid=1 interpolation=Bilinear stack"
)
IJ
.
run
(
vector_imp
,
"Rotate..."
,
"angle=-90 grid=1 interpolation=Bilinear stack"
)
#Convert all images to RGB
unregistered_merged_channels_imp
=
RGBStackMerge
.
mergeChannels
([
unregistered_tdTom_imp
,
unregistered_GC6s_imp
,
unregistered_GC6s_imp
],
False
)
registered_merged_channels_imp
=
RGBStackMerge
.
mergeChannels
([
registered_tdTom_imp
,
registered_GC6s_imp
,
registered_GC6s_imp
],
False
)
IJ
.
run
(
unregistered_merged_channels_imp
,
"RGB Color"
,
"slices"
)
IJ
.
run
(
registered_merged_channels_imp
,
"RGB Color"
,
"slices"
)
IJ
.
run
(
vector_imp
,
"RGB Color"
,
"slices"
)
#Combine image into one (stacked on top of each other)
two_combined_stack
=
stack_combiner
.
combineVertically
(
unregistered_merged_channels_imp
.
getStack
(),
vector_imp
.
getStack
())
three_combined_stack
=
stack_combiner
.
combineVertically
(
two_combined_stack
,
registered_merged_channels_imp
.
getStack
())
#Save result
file_saver_combined_image
=
FileSaver
(
ImagePlus
(
'combined'
,
three_combined_stack
))
file_saver_combined_image
.
saveAsTiffStack
(
outdir
+
'/column.tif'
)
##Calculate baseline average intensity
#n = unregistered_GC6s_imp.getStackSize()
#unregistered_GC6s_avg_imp = z_proj.run(unregistered_GC6s_imp,"avg")
#registered_GC6s_avg_imp = z_proj.run(registered_GC6s_imp,"avg")
#unregistered_tdTom_avg_imp = z_proj.run(unregistered_tdTom_imp,"avg")
#registered_tdTom_avg_imp = z_proj.run(registered_tdTom_imp,"avg")
#
#dF_imp = ic.run("Subtract create 32-bit stack", unregistered_GC6s_imp, unregistered_GC6s_avg_imp)
#dF_over_F_imp = ic.run("Divide create 32-bit stack", dF_imp,unregistered_GC6s_avg_imp)
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