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R6289/fiji_script_vertical_combination.py
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fiji_script_vertical_combination.py
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#@String parameter_file
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 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()
#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(files['GC6s_registered'])
registered_GC6s_imp = opener.openTiffStack(registered_GC6s_info)
registered_tdTom_info = opener.getTiffFileInfo(files['tdTom_registered'])
registered_tdTom_imp = opener.openTiffStack(registered_tdTom_info)
vector_info = opener.getTiffFileInfo(files['vectors_out'])
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()))
#Convert all images to RGB
unregistered_merged_channels_imp = RGBStackMerge.mergeChannels([unregistered_tdTom_imp, unregistered_GC6s_imp, None],False)
registered_merged_channels_imp = RGBStackMerge.mergeChannels([registered_tdTom_imp, registered_GC6s_imp, None],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(files['column_out'])
##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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